7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Maybe the file was not transferred correctly to your desktop PC. From: Gianluca Interlandi (gianluca_at_u. washington. > > > > Forget about creating a pdb file. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. Biochemistry. washington. edu > <mailto:gianluca_at_u. Is it appropriate to use a > >thermostat and barostat (CPT) while performing a constant force orRe: Force field design. >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. Gianluca, Yes, I think that a higher damping constant will indeed slow down conformational sampling. On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi < gianluca_at_u. washington. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. From: Gianluca Interlandi (gianluca_at_u. Kidd, 2 Isolde Le Trong, 3 Veronika Tchesnokova, 1 Olga Yakovenko, 2 Matt J. edu) Date: Thu Apr 05 2012 - 15:44:43 CDT Next message: Gianluca Interlandi: "Re: DCD" Previous message: Jérôme Hénin: "Re: changing harmonic restraints (colvars)" Next in thread: Gianluca Interlandi: "Re: DCD" Reply: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ]. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. It's > slightly faster but still not that much faster than running on 16 CPU cores. From: Gianluca Interlandi (gianluca_at_u. washington. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > Dear Marcos, > > Thanks a lot for your answer and for offering me your help. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". washington. edu> wrote: > Hi, > > I have a question concerning running NAMD on a CUDA cluster. uiuc. She joined Schiller DuCanto & Fleck LLP in 1999 as a law clerk and became partner with the firm in 2009. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. VMD-L Mailing List. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Re: Langevin damping coefficient. Here they are: a. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. I thought I will see in my output file the energies stored at times 0 fs, 500 fs,. Display options. The simulations were not performed at constant velocity > but at constant force. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected] on Abe" In reply to: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" Messages sorted by: [ attachment ] The amount of computational work that you have for the nonbonded short-range interactions (which is the dominant part of the overallConvert solvated CHARMM PDB + PSF to Amber. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. >Re: Vibrational mode analysis. washington. washington. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. 6 version, although I am not running the cluster at full load yet. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. washington. washington. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Re: namd ibverbs. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. From: Gianluca Interlandi (gianluca_at_u. Proteins 78, 2506–2522 [PMC free article] [Google Scholar]Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. From: Gianluca Interlandi (gianluca_at_u. C; the more troublesome part is the lack of long-range electrostatic treatments. I am > using the option "wrapAll on". washington. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. washington. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. The simulations were not performed at constant velocity > but at constant force. >Gianluca Interlandi (Property Manager Baroque Apartments) Hosting since October 2020. It's > slightly faster but still not that much faster than running on 16 CPU cores. From: Gianluca Interlandi (gianluca_at_u. washington. PMID: 37700555; DOI: 10. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. washington. washington. From: Gianluca Interlandi <gianluca_at_u. On 6 May 2009, at 11:04, Gianluca Interlandi wrote: > Thanks Anton for your answer. washington. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. I would be > happy if somebody could point me out to some scripts which help me perform Hemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. Balcony. I needed to install the 'patch' program. <br> <br>1999 March: Degree in modern languages result 107/110 - University of Catania, Italy with a degree thesis on Irish. I also ran a non-CUDA job on Forge > using 16 CPUs. It's > slightly faster but still not that much faster than running on 16 CPU cores. Kisiela, # 1 , * Hovhannes Avagyan, # 1 Della Friend, 2 Aachal Jalan, 1 Shivani Gupta, 3 Gianluca Interlandi, 3 Yan Liu, 4 Veronika Tchesnokova, 1 Victoria. at 298. Bioengineering. 15 K 1 KT = 2. There have been over 180 downloads and no complaints so far. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Mon, Aug 26, 2013 at 12:56 PM, Gianluca Interlandi < gianluca_at_u. gov) Date: Fri Jun 18 2004 - 14:48:36 CDT Next message: Gianluca Interlandi: "Re: recentering protein in the waterbox" Previous message: Jerry Ebalunode: "recentering protein in the waterbox" Messages sorted by: [ attachment ] Hello, I'm running namd and am getting the following errors as itsIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. INVENTING THE FUTURE OF MEDICINE. In reply to: Gianluca Interlandi: "RE: Force field design" Messages sorted by: [ attachment ] Ouch. 100% refund of amount payable if you cancel at least 14 days before check-in. washington. {Gianluca Interlandi and Svava K Wetzel and Giovanni Settanni and Andreas Pl{"u}ckthun and Amedeo Caflisch}, journal={Journal of molecular biology}, year={2008},. Languages spoken: English. washington. Next in thread: Gianluca Interlandi: "Re: NAMD 2. edu> > wrote: > are other people also using those GPUs? > >Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] kcal/mol/A^2 is actually units for a force constant (for a spring for. washington. edu> wrote: > A few of the simulations aborted with the following message: >> "ERROR: Atoms moving too fast; simulation has become unstable. washington. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. 7 ns/day, which seems decent given the system size. uiuc. washington. I made those videos seven years ago. 7 released. washington. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. In the NAMD folder that you downloaded there >> is a file called "notes. washington. washington. Re: Help building a desktop for namd. washington. I doubt that there is a way to have NAMD output theFrom: Gianluca Interlandi (gianluca_at_u. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. From: Gianluca Interlandi (gianluca_at_u. washington. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. washington. washington. In the text field you can enter your atom selection, e. Gianluca Interlandi [email protected] orcid. washington. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. washington. Reply: Gianluca Interlandi: "Re: Regarding thermostats" Reply: Marcos Sotomayor: "Re: Regarding thermostats" Messages sorted by: [ attachment ] Dear NAMD users, Lately in the lab we have been discussing about which thermostat use in our simulations. edu> wrote: > What are your simulation parameters: >> >> timestep (and also any multistepping values) >> > 2 fs, SHAKE, no multistepping > > > cutoff (and also the pairlist and PME grid spacing) >> > 8-10-12 PME grid spacing ~ 1 A > > Interlandi G. Electrical Engineering. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. From: Buddhadev Maiti (bmaiti_at_gsu. Just a good MD toy ! Victor owner-namd-l_at_ks. > Auftrag von Gianluca Interlandi > Gesendet: Freitag, 13. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. washington. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Eric Klavins Professor. 6 version, although I am not running the cluster at full load yet. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. washington. edu) Date: Mon Apr 11 2011 - 14:41:28 CDT Next message: Axel Kohlmeyer: "Re: Help building a desktop for namd" Previous message: Buddhadev Maiti: "(no subject)" In reply to: Axel Kohlmeyer: "Re: Help building a desktop for namd" Next in. " Previous message: Gianluca Interlandi: "multicore vs ibverbs" Messages sorted by: [ attachment ] Dear NAMD list, I am a bit. On Tue, 19 Oct 2010, Gianluca Interlandi wrote: > Hi Jim, > > This is great! Is there also a compiled version for Clustermatic 5? > > Thanks, > > Gianluca > > On Tue, 19 Oct 2010, Jim Phillips wrote: > >> Hi all, >> >> I pushed 2. It is experimentally knownReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. Choose File -> Save Coordinates. Stereo system. From: Gianluca Interlandi (gianluca_at_u. 26055 Abstract The blood protein von Willebrand factor (VWF) is a key link between inflammation and pathological thrombus formation. 7 On Wed, Sep 18, 2013 at 11:43:49AM -0700, Gianluca Interlandi wrote: > Dear VMD list, > > I think that this question was asked previously. Check the NAMD log! Any errors or warnings?"wrapAll on" with a complex. Author Profile. washington. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. washington. 478 KJ/mol = 0. Member since 2014. edu]Reply All Saturday,. You should simulate it in explicit water (or try one of the implicitGianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. Sorry for posting it here, but maybe somebody might have tried it, too. washington. July; 84 (7):990–1008. washington. edu) Date: Wed Oct 20 2010 - 15:33:33 CDT Next message: jnsong: "how to cenvert NAMD binary coordinate file to text file" Previous message: Jim Phillips: "Re: NAMD 2. (2010) The catch bond mechanism between von Willebrand factor and platelets investigated by molecular dynamics simulations. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. washington. From: Gianluca Interlandi [gianluca_at_u. 26588 Item in Clipboard Cite. Abstract. washington. 7 ns/day, which seems decent given the system size. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. Thanks for the reply. washington. washington. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. Chemistry. edu] > Sent: Thursday, April 05, 2012 5:04 PM > To: Buddhadev Maiti > Cc: Jérôme Hénin; namd-l_at_ks. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. Contact host. washington. C; the more troublesome part is the lack of long-range electrostatic treatments. " Messages sorted by: [ attachment ] On Sun, 2009-08-30 at 12:11 -0700, Gianluca Interlandi wrote: > Thank you Mike for sharing your information. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. VMD-L Mailing List. Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations. washington. 7 with the PLUMED patch" Previous message: Alex Liu: "Fix atoms-Colvars" Next in thread: Gianluca Interlandi: "Re:. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. washington. e. Kid friendly. Gianluca Interlandi Curriculum Vitae Department of Bioengineering, University of Washington, 1705 NE Pacific Street, 98195 Seattle, WA, [email protected]: Gianluca Interlandi (gianluca_at_u. Gianluca Interlandi, research assistant professor, and Wendy Thomas, professor: Antibody Dependent Enhancement, a type of immune system backfiring that causes increased infection in cells, is likely responsible for disappointing results on experimental vaccines for SARS and MERS, and. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. Next message: Gianluca Interlandi: "Infiniband and PME gridsize" Previous message: nordgren_at_sas. uiuc. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. washington. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. 10. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2. From: Gianluca Interlandi (gianluca_at_u. But not now. NAMD doesn't that i know of. 0 and 2. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. edu> Subject: Re: namd-l: "wrapAll on" with a complex Gianluca: Using VMD with the attached script should solve that. These are the lastIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. View Gianluca Interlandi’s profile on LinkedIn, the world’s largest professional community. washington. Semantic Scholar's Logo. 7 released" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the. The simulations were not performed at constant velocity > but at constant force. com) Date: Wed Sep 18 2013 - 14:48:11 CDT Next message: Gianluca Interlandi: "Re: Open VMD from a remote host" Previous message: John Stone: "Re: Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Gianluca. edu on behalf of Gianluca Interlandi [gianluca_at_u. Both > simulations were started from X-ray structures. From: Gianluca Interlandi (gianluca_at_u. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. From: Gianluca Interlandi (gianluca_at_u. You should simulate it in explicit water (or try one of the implicitRe: Protein in/out of box. washington. 478 KJ/mol = 0. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. 7b1 on NCSA Abe. washington. I needed to install the 'patch' program. edu) Date: Thu Mar 17 2011 - 17:58:46 CDT Next message: Giacomo Fiorin: "Re: GBIS and ABF" Previous message: Branko: "GBIS and ABF" Messages sorted by: [ attachment ] Dear Jim, Do you happen to have the charmm++. washington. On Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). Reply: Gianluca Interlandi: "Re: Cuda benchmarks namd2. From: Gianluca Interlandi (gianluca_at_u. Education/training Institution and location Dates attended Degree Conferred Field of study Interlandi G, Thomas WE. washington. washington. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. washington. Stenkamp, 3 Wendy E. Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne, Christopher G: "Re: Force field design" Messages sorted by: [ attachment ] If you are familiar with the CHARMM program, a good resource is:. . , "not. From: Gianluca Interlandi (gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi <gianluca_at_u. washington. washington. View the profiles of people named Gianluca Interlandi. , Thomas W. double. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. uiuc. I doubt that there is a way to have> 2011/6/29 Gianluca Interlandi <gianluca_at_u. At the point of breaking the temperature raises of a few> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. Education/training Institution and location Dates attended Degree Conferred Field of studyGianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. Just a good MD toy ! Victor owner-namd-l_at_ks. Electrical. During the minimization and equilibriation with protein constrained, the > disulfide bond breaks. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. Rooms and beds. In reply to: Gianluca Interlandi: "Re: namd ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. edu) Date: Thu Jan 06 2011 - 16:55:03 CST Next message: Gianluca Interlandi: "Re: Compiling NAMD 2. uiuc. washington. edu) Date: Thu Apr 30 2009 - 12:15:37 CDT Next message: bo liu: "Re: Optimizing configuration option for fast calculations" Previous message: Jerome Henin: "Re: Benzene PSF" In reply to: Peter Freddolino: "Re: NAMD 2. edu> > wrote: > Roy, > > I think that you are confusing two things. I wanted to briefly update here on my > experience. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). > > Forget about creating a pdb file. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. I would be > happy if somebody could point me out to some scripts which help me performOn Fri, Jun 27, 2008 at 9:16 PM, Gianluca Interlandi <gianluca_at_u. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. washington. From: Axel Kohlmeyer (akohlmey_at_gmail. Skip to search form Skip to main content Skip to account menu. Policies. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. I have to run following commands 2 times in tcl. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field > parameters? > > Thanks, > Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" Next in thread: Gianluca Interlandi: "Re: query about wrapped coordinates" Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" From: Gianluca Interlandi (gianluca_at_u. edu Search for more papers by this author> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. washington. washington. I would be > happy if somebody could point me out to some scripts which help me performHemostasis in vertebrates involves both a cellular and a protein component and von Willebrand factor evolved in the ancestral vertebrate following the divergence of the urochordates some 500 million years ago and that it acquired increasing complexity though sequential insertion of functional modules. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. Juli 2012 00:26 > An: Aron Broom > Cc: NAMD list > Betreff: Re: namd-l: Running NAMD on Forge (CUDA) > > Yes, I was totally surprised, too. washington. washington. washington. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. edu> wrote:Reply: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi <gianluca_at_u. 1. From: Gianluca Interlandi (gianluca_at_u. uiuc. edu) Date: Wed May 06 2009 - 11:04:21 CDT Next message: Anton Arkhipov: "Re: Langevin damping coefficient" Previous message: Benjamin Stauch: "diffusion / fex peptide problem" In reply to: Anton Arkhipov: "Re: Langevin damping coefficient" Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. washington. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. Re: Yet another NAMD speed concerns. E-mail: [email protected],. 7 with the PLUMED patch" Messages sorted by: [ attachment ] I found the problem. From: Gianluca Interlandi (gianluca_at_u. If I > want to use all 6 CUDA devices in a node, how many processes is it > recommended to spawn?> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. 15 K 1 KT = 2. . The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. I was getting 2. washington. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Chemistry. prm". edu) Date: Thu Apr 07 2011 - 13:57:41 CDT Next message: Axel Kohlmeyer: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Axel Kohlmeyer: "Re: Abe versus Lincoln"From: Gianluca Interlandi (gianluca_at_u. Gianluca On Sun, 30 Aug 2009, Gianluca Interlandi wrote: > Thanks Axel, > > I have also compared the cost of a GPU equiped PC versus a dual Quadcore PC. washington. uiuc. washington. > However, topology and parameters for water and ions are. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. edu) Date: Tue Oct 03 2006 - 00:01:37 CDT Next message: Ugur Akgun: "SMD From Force to Free Energy" Previous message: JC Gumbart: "Re: How can I do protein complex's simulation?" In reply to: Gianluca Interlandi: "SMD and. edu> > wrote: > are other people also using those GPUs? > >In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. Sarah Keller Professor. washington. From: Gianluca Interlandi (gianluca_at_u. Hope the video helps, but now I'm embarrassed. Bidet · Toilet · Shower. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. C; the more troublesome part is the lack of long-range electrostatic treatments. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. washington. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. RE: Force field design. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Gianluca Interlandi Research Assistant Professor. Previous message: Gianluca Interlandi: "NAMD 2. I would be > happy if somebody could point me out to some scripts which help me performOn Thu, 5 Apr 2012, Gianluca Interlandi wrote: > What is the advantage of the multicore version of charm++ versus net-linux? > Is multicore faster if I'm running for example on a 32-core magny-Cours AMDFrom: Gianluca Interlandi (gianluca_at_u. Entertainment. It's > slightly faster but still not that much faster than running on 16 CPU cores. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. Hemostasis in vertebrates involves both a. From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. washington. washington. That's why one wants to use a low value for the damping constant, in principle. g. On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. In reply to: Gianluca Interlandi: "Compiling NAMD 2. washington. -michael On Jun 15, 2006, at 5:31 PM, Gianluca Interlandi wrote:> 2011/6/29 Gianluca Interlandi <gianluca_at_u. , and Thomas W. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. From: Gianluca Interlandi [gianluca_at_u. Gianluca Interlandi.