Re: [gmx-users] re-sort frames by RMSD
Hello Joao! Thanks for the info! Actually, I want to re-sort the actual frames in the trajectory. -- View this message in context: http://gromacs.5086.x6.nabble.com/re-sort-frames-by-RMSD-tp5015416p5015450.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Hehe that is a good point! Indeed, he says that multiple time stepping is a better compromise on increasing speed. However, he says the NAMD multiple step scheme uses 4fs for long range electrostatics, while using 1fs for bonded interactions. So actually, the theoretical root of the disagreement seems to be on the validity of using length constraints for all bonds. The gist of what he was saying is that moving to a larger global timestep could cause you to miss interactions, effectively skipping over small local minima, and deviate from sampling the real hypersurface. He seemed OK with fixing the length of heavy-atom to hydrogen bonds and doing production at 2fs, but not fixing heavy-to-heavy bond lengths. Virtual sites + global 4fs seems taboo. For the same protein, I have a workflow using LINCS all-bonds @ 2fs for equilibration and production, and a workflow using LINCS all-bonds + vsite aromatics @ 4fs for equilibration and production. What parameters should I show for comparison? On Tue, Feb 11, 2014 at 3:00 PM, Szilárd Páll-2 [via GROMACS] ml-node+s5086n5014465...@n6.nabble.com wrote: On Tue, Feb 11, 2014 at 12:11 PM, unitALX [hidden email]http://user/SendEmail.jtp?type=nodenode=5014465i=0 wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I would you mind asking your friend whether multiple time stepping disgusts him too? :) -- Szilárd I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [hidden email]http://user/SendEmail.jtp?type=nodenode=5014465i=1. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [hidden email]http://user/SendEmail.jtp?type=nodenode=5014465i=2. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461p5014465.html To unsubscribe from Justifying 4fs production runs after 1fs equilibrations?, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5014461code=YWxlYy56YW5kZXJAZ21haWwuY29tfDUwMTQ0NjF8MTcxMDQ5NjUwOA== . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble
Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations?
Yar, I understand. However, because of the differences in software experience (NAMD / GROMACS), presenting literature references is not as effective as I thought it would be, historical inertia and spirited argumentation is having more weight than I thought it would, and in between what is published for GROMACS and his best practice methods for NAMD, there is a gray area for which is effectively being biased towards NAMD style protocols (or what have you) and while you are correct in the long-term thermodynamic limit of publishing work, I have kinetic barrier to overcome in explaining something to someone who has seniority over me in my place of work and whose advice gives the de facto direction of the work I do. Hence why I am asking this more gray question of how to justify and explain across the software divide what I think are faster but valid choices for protocols. It is with considerable uneasiness that I see explanations being made in this gray area that are not consistent with the papers I am reading. To be more blunt about my situation, we are in a gray area on the choice of a homology model whose stability is being assessed by dynamics, and I am hearing people say things like well its a gray area, we can just argue it this way, or that way, and then we'll submit the results to a journal, and if they don't agree, we'll just submit the same work to another journal. I face a higher burden of proof than the textbook approach. Please advise. On Tue, Feb 11, 2014 at 4:12 PM, TomPiggot [via GROMACS] ml-node+s5086n5014470...@n6.nabble.com wrote: Hi, Personally I would also ask your colleague if he could also provide evidence (e.g. published papers) to back up what he is saying to you (i.e. that it is necessary to use a 1 fs timestep with an NVE ensemble to achieve acceptable results). This way, you can make an informed decision based upon the available evidence you can find, rather than simply upon one persons view point. I would suggest the he will find it difficult to come up with such evidence for your case of a straight forward MD simulation. You should also remember that you are the one that will need to be able to defend (to an examiner or reviewer) what you have done and why. Simply because the postdoc told me it was the correct thing to do will (unfortunately) not be good enough! Cheers Tom From: [hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=0[[hidden email] http://user/SendEmail.jtp?type=nodenode=5014470i=1] on behalf of Szilárd Páll [[hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=2] Sent: 11 February 2014 13:33 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Justifying 4fs production runs after 1fs equilibrations? On Tue, Feb 11, 2014 at 12:11 PM, unitALX [hidden email]http://user/SendEmail.jtp?type=nodenode=5014470i=3 wrote: Helllo all! In my general situation, I have a batch of homology models that I would like to assess for stability by molecular dynamics. I am working with a postdoc in my lab who was extensive experience with NAMD, but does not use GROMACS. We have been developing protocol for these MD simulations, but we had some different views on equilibration and production. Equlibration My friend is recommending that I do equilibration for 500ps @ 1fs with no constraints. I have no real objection to that, but he made it seem like the results might be quite different than an equilibration for 200ps @ 2fs with LINCS all-bonds. Would it make a critical difference? Production I was excited by the performance possible with LINCS all-bonds, -vsite aromatics @ 4fs, but my friend looks at 4fs with disgust. I would you mind asking your friend whether multiple time stepping disgusts him too? :) -- Szilárd I responded with arguments from the GROMACS 4 paper, and a paper called Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems re: the relationship between the period of the fastest vibration and largest allowable timestep, but he seems quite convinced that for publication, only 1fs and possibly 2fs production runs (preferably without barostat and thermostat??) are acceptable. The suggestion to drop the barostat and thermostat for production follows the philosophy that if your minimization and equilibration is properly done, then the system should be stable in production without pressure temperature control. I'm having a hard time finding better literature justifications for usage of LINCS all-bonds @ 2fs, and certainly for -vsites @ 4fs; PT control seems quite standard in publications using GROMACS. Can you suggest any papers or calculations I can do to show the validity of these options? -- View this message in context: http://gromacs.5086.x6.nabble.com/Justifying-4fs-production-runs-after-1fs-equilibrations-tp5014461.html
[gmx-users] graphics card fail during mdrun
Hello! I was running a simulation using both of the graphics cards on my desktop (I have one Tesla C2075 and one Quadro 2000, which also handles monitor output). I am pretty sure the Quadro 2000 has failed this morning, and I was wondering, what happens to an mdrun in progress when one of the graphics cards fails? -- View this message in context: http://gromacs.5086.x6.nabble.com/graphics-card-fail-during-mdrun-tp5014075.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
