Re: [gmx-users] difference in potenital energy on desktop and server run
Hi Justin The bilayer is full solvated. It has 128 ceramide and 5120 water molecules (40 water molecule per ceramide). I ran same simulation on my desktop machine it is working properly, properties such as potential energy and area per lipid converse very nicely. Is there any problem with server or running on multiple thread. -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014839.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] difference in potenital energy on desktop and server run
thanx Dr. Vitaly could you please explain me what did you mean by incorrectly treating of periodicity? Is it related to update of neighbour list? My system is periodic in 3 dimension and pressure coupling is anisotropic. -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014840.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] difference in potenital energy on desktop and server run
I am using gromacs 4.6.5. Surprisingly system is stable at such high potential energy. I created bilayer system using packmol then solvated it with water using genbox. I did energy minimization using following command grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr mdrun -c -v -deffnm min The resulted potential energy of system was negative (~ 2x 10^-5 ). Then I performed NPT run using following command grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr mdrun -c -v -deffnm NPT The resulted structure and system was stable but the potential energy of the system was highly positvie (~ 10^5). Just for curiosity I took resulted NPT.gro structure and ran NPT simulation on my desktop which has same version of GROMACS (same precision). Surprisingly the total energy was negative after few ps run and converse to around order of ~ -10^5. I have attached my input .mdp files for energy minimization and NPT MD run. On Wed, Feb 26, 2014 at 4:41 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5014819...@n6.nabble.com wrote: On 2/26/14, 12:51 AM, gupta.rakesh082 wrote: Dear allI performed MD simulation of lipid bilayer on my desktop it is giving correct results and negative potential energy (~ -10^5) but when I ran the same simulation on a server using multi thread (-nt 8), It is giving positive potential energy (~ 10^5). Initially I thought it might be problem with mpi to check this I ran simulation on cluster with single thread but still potential energy is positive.Any help would be appreciated If the potential energy was that high, I would suspect the system crashed - did it? What were you running, EM or MD? If the latter, did you provide the correct, energy-minimized structure to grompp when creating the .tpr file for the run? Detailed commands and actual output would be useful here, otherwise it's all guesswork. Also, what version of Gromacs are you using? -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=5014819i=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=5014819i=1. -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014819.html To unsubscribe from difference in potenital energy on desktop and server run, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5014813code=Z3VwdGEucmFrZXNoMDgyQGdtYWlsLmNvbXw1MDE0ODEzfDI5OTY2MzU1MA== . 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 -- -- Regards RAKESH GUPTA == ME- Chemical Engineering Indian Institute of Science Bangalore-560012 === (M) +91-9611187322 npt.mdp (3K) http://gromacs.5086.x6.nabble.com/attachment/5014826/0/npt.mdp em.mdp (1K) http://gromacs.5086.x6.nabble.com/attachment/5014826/1/em.mdp -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014826.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] difference in potenital energy on desktop and server run
EM RUNSteepest Descents converged to machine precision in 2820 steps,but did not reach the requested Fmax 10.Potential Energy = -2.9268122e+05Maximum force = 1.9479546e+02 on atom 123Norm of force = 6.3931437e+00grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tprmdrun -c -v -deffnm min g_energy -f min.edr -o npt_potenital.xvg10 0Statistics over 2818 steps [ 0. through 2817. ps ], 1 data setsAll statistics are over 2225 points (frames)Energy Average Err.Est. RMSD Tot-Drift---Potential -287434 28006986.15 -18110.5 (kJ/mol)NPT RUNgrompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tprmdrun -nt 8 -c -v -deffnm NPT g_energy -f NPT.edr -o npt_potenital.xvg10 0Statistics over 1001 steps [ 0. through 2. ps ], 1 data setsAll statistics are over 11 pointsEnergy Average Err.Est. RMSD Tot-Drift---Potential 168770 130031030.1 -6644.57 (kJ/mol)I am surprised to see that at such huge potential energy my simulation box is still stable. Desktop RunI took generated NPT.gro file in previous run and performed a small 200 ps npt simulation on my desktop machine using following commmand.grompp -f NPT.mdp -c NPT.gro -p cer.itp -o NPTdesktop.tprmdrun --c -v -deffnm NPTdesktopg_energy -f NPTdesktop.edr -o NPTdesktop_potential.xvgStatistics over 11 steps [ 0. through 200. ps ], 1 data setsAll statistics are over 1001 pointsEnergy Average Err.Est. RMSD Tot-Drift---Potential -234831 47582.555117.566 (kJ/mol)This time potential energy became negative after few ps and converse to value around order of ~ -2x 10^5. -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014832.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] difference in potenital energy on desktop and server run
EM RUN Steepest Descents converged to machine precision in 2820 steps, but did not reach the requested Fmax 10. Potential Energy = -2.9268122e+05 Maximum force = 1.9479546e+02 on atom 123 Norm of force = 6.3931437e+00 grompp -f em.mdp -c cerblayer.gro -p cer.itp -o min.tpr mdrun -c -v -deffnm min g_energy -f min.edr -o npt_potenital.xvg 10 0 Statistics over 2818 steps [ 0. through 2817. ps ], 1 data sets All statistics are over 2225 points (frames) Energy Average Err.Est. RMSD Tot-Drift --- Potential -287434 28006986.15 -18110.5 (kJ/mol) NPT RUN grompp -f NPT.mdp -c min.gro -p cer.itp -o NPT.tpr mdrun -nt 8 -c -v -deffnm NPT g_energy -f NPT.edr -o npt_potenital.xvg 10 0 Statistics over 1001 steps [ 0. through 2. ps ], 1 data sets All statistics are over 11 points Energy Average Err.Est. RMSD Tot-Drift --- Potential168770 130031030.1 -6644.57 (kJ/mol) I am surprised to see that at such huge potential energy my simulation box is still stable. Desktop Run I took generated NPT.gro file in previous run and performed a small 200 ps npt simulation on my desktop machine using following commmand. grompp -f NPT.mdp -c NPT.gro -p cer.itp -o NPTdesktop.tpr mdrun --c -v -deffnm NPTdesktop g_energy -f NPTdesktop.edr -o NPTdesktop_potential.xvg Statistics over 11 steps [ 0. through 200. ps ], 1 data sets All statistics are over 1001 points Energy Average Err.Est. RMSD Tot-Drift --- Potential -234831 47582.555117.566 (kJ/mol) This time potential energy became negative after few ps and converse to value around order of ~ -2x 10^5. -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813p5014834.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] difference in potenital energy on desktop and server run
Dear allI performed MD simulation of lipid bilayer on my desktop it is giving correct results and negative potential energy (~ -10^5) but when I ran the same simulation on a server using multi thread (-nt 8), It is giving positive potential energy (~ 10^5). Initially I thought it might be problem with mpi to check this I ran simulation on cluster with single thread but still potential energy is positive.Any help would be appreciated -- View this message in context: http://gromacs.5086.x6.nabble.com/difference-in-potenital-energy-on-desktop-and-server-run-tp5014813.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.
