Re: [gmx-users] Erro in SMD simulation..
Thank you Justin so much... In case of this system rectangular (10x10x25) is working.. SMD is over with out any error.. Thank you.. On Wed, Apr 2, 2014 at 12:03 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5015557...@n6.nabble.com wrote: On 4/1/14, 2:18 PM, Kalyanashis wrote: Thank you so much Justin. Now I am trying with a rectangular box. I don not whether it will work or not. There shouldn't be any guesswork involved. You know what the initial COM separation is (or you can easily calculate it or wait for grompp to print it out), and you know from pull_rate1 and the number of steps what the maximum displacement should be, so you can plan accordingly. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [hidden email] http://user/SendEmail.jtp?type=nodenode=5015557i=0 | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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=5015557i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/Erro-in-SMD-simulation-tp5015535p5015557.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from Erro in SMD simulation.., click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5015535code=a2FseWFuLmNoZW0uaW5AZ21haWwuY29tfDUwMTU1MzV8NTkxMDYyNTYz . 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%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- Kalyanashis Jana email: kalyan.chem...@gmail.com -- View this message in context: http://gromacs.5086.x6.nabble.com/Erro-in-SMD-simulation-tp5015535p5015936.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] Reproducibility in free energy calculations.
On 4/19/14, 1:16 AM, sujithkakkat . wrote: Hello Justin, I tried the free energy calculations in your tutorial at different sets of conditions. Also I repeated a simulation at the same conditions with same parameters, thrice on the same computer on same number of processors. The results in the three cases where different (4.16 +/- 0.19 , 4.36 +/-0.14 , 4.54 +/-0.15 kJ/mol ) . I am not surprised, since I thought that this might happen to a small system (241 water + 1 methane). However, I want to be sure that this is OK. I guess in cases like this I should go for an average value of many runs. Offhand, I would have expected slightly better agreement between the runs, but there are tons of factors at play, so the outcome seems very plausible and reasonably consistent. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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] Reproducibility in free energy calculations.
Mean of the three calculations is 4.35, standard error is 0.19. So this seems statistically consistent. If you want to get more consistent results, you'll need to run longer until the estimated statistical uncertainty is lower. Also, the estimated uncertainty is often an underestimate (BAR often underestimates by 20-30%). On Sat, Apr 19, 2014 at 9:05 AM, Justin Lemkul jalem...@vt.edu wrote: On 4/19/14, 1:16 AM, sujithkakkat . wrote: Hello Justin, I tried the free energy calculations in your tutorial at different sets of conditions. Also I repeated a simulation at the same conditions with same parameters, thrice on the same computer on same number of processors. The results in the three cases where different (4.16 +/- 0.19 , 4.36 +/-0.14 , 4.54 +/-0.15 kJ/mol ) . I am not surprised, since I thought that this might happen to a small system (241 water + 1 methane). However, I want to be sure that this is OK. I guess in cases like this I should go for an average value of many runs. Offhand, I would have expected slightly better agreement between the runs, but there are tons of factors at play, so the outcome seems very plausible and reasonably consistent. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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. -- 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] about tutorial on virtual sites
Hello Justin, I found that in the virtual sites section of your tutorial, the energy values of the system large positive . You had warned in the topology file that the choice of the partial charges used are not guaranteed to work always with OPLSAA . However, the momentum of inertial values points indicate proper dynamics of the system. Is the positive potential energy an out come of using the OPLSAA forcefield ? Is it normal to have positive potential energy? Regards, Sujith. -- 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] running parallel simulations on different of cores
Dear gromacs users, I have been working on gromacs package for performing md simulations. recently i have started using cluster with 2 nodes with 64 cores each. I am eager to know whether a job run on 32 cores for few ns and later i continue the same job on 64 cores (or vice versa), will show any difference in the results in terms of energies or the conformational changes. thanks in advance -- 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] Specifying the number of OpenMP threads that g_hbond uses
Hi, From the web page http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x , it looks like parallelization for g_hbond (via OpenMP) was added in version 4.6.x. What is a typical command to run g_hbond in parallel? Since I mostly have experience with Gromacs 4.5.5 (which for mdrun has auto MPI threading as the default parallelization, which means I only have to specify the number of threads with -nt), I am not sure how to launch OpenMP for g_hbond in 4.6.x. When I just run g_hbond in 4.6.1 with no extra flags, the output says, Frame loop parallelized with OpenMP using 8 threads. Is there any way to change the number of OpenMP threads that g_hbond uses? Thanks so much! Andrew DeYoung Carnegie Mellon University -- 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] how to fix center of mass
Dear Gromacs Users, I am simulating a polymer membrane, which has two boxes of water on both sides. Polymer membrane position is shifting a lot even though I used comm_mode = linear Is there a way to fix the center of the mass of polymer membrane? Thanks a lot for the suggestions! Thom -- 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] GCMC?
Dear Gromacs Developers Can some gromacs new version do Grand Canonical Monte Carlo (GCMC) simulations? Thanks! Thomas -- 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] GCMC?
No On Apr 19, 2014 8:17 PM, Tom dna...@gmail.com wrote: Dear Gromacs Developers Can some gromacs new version do Grand Canonical Monte Carlo (GCMC) simulations? Thanks! Thomas -- 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. -- 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] about tutorial on virtual sites
On 4/19/14, 11:06 AM, sujithkakkat . wrote: Hello Justin, I found that in the virtual sites section of your tutorial, the energy values of the system large positive . You had warned in the topology file that the choice of the partial charges used are not guaranteed to work always with OPLSAA . However, the momentum of inertial values points indicate proper dynamics of the system. Is the positive potential energy an out come of using the OPLSAA forcefield ? Is it normal to have positive potential energy? Yes, that is normal. Most gas-phase simulations will have a positive energy. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
