Re: [gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Hi again, I used the Martini version of the force-field. The difference in volume is only about 1 percent, but still much larger than the fluctuations which are about 0.1 percent. The effect is very systematic though, and it can be disturbing if you have carelessly run simulations with different versions and try to compare the results :) The reason why I am testing this is that we observed a similar effect with other force fields too, and could not explain it. For example, area per lipid values for lipid bilayers (all-atom) displayed a similar dependency on gromacs version, but now with 5 to 10 percent differences. I am not yet sure if this is caused by the same effect at all, but continuing to test on it. If anybody has seen similar effects and/or has other possible explanations, would be nice to hear them. Regards, Perttu On Tue, 8 Jan 2008 15:39:51 +0200 (EET) Perttu Niemela [EMAIL PROTECTED] wrote: Hi All, In December here was a short discussion about a water system, for which gromacs versions 3.2.1 and 3.3.1 produced different average volumes. I have experienced similar thing with Marrink's coarse grained water (about 1500 beads in the box), but to opposite direction. Just by curiosity: which version the ff you use? My test runs with gromacs 3.1.4 and 3.2.1 always give a larger average volume than versions 3.3.1. and 3.3.2. The difference is much larger than the fluctuations. I use berendsen barostat (isotropic; p = 1 atm) and thermostat (T=300K). In my simulations, the off-diagonal terms of the virial are very close to zero. Additionally, I have tested using simple cutoffs instead of switch/shift functions, but it does not affect the general conclusion. How much is the difference you observe and which percentage of the volume does this represent? Can it be that the difference in calculating the kinetic energy (and temperature) leads to the observed volume difference? I did a quick test to modify the code of gromacs v. 3.3.1 such that it calculates kinetic energy exactly like in v. 3.2.1, and the volume jumps back up. Can somebody please confirm, if this is expected? I cannot fully understand how a more exact calculation of the kinetic energy would lead to a significant change of the average volume (?) Well a change in temperature should affect the volume of course, so the change in estimation of the kinetic energy will affect the volume but the effect should be very small! XAvier ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Dear users, I had posted this question earlier too but did not get any response. I am re-posting it hoping someone can clarify this for me. I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (spc/e 10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I used SETTLE to maintain water geometry. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
sapna sarupria wrote: Dear users, I had posted this question earlier too but did not get any response. I am re-posting it hoping someone can clarify this for me. I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (spc/e 10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I used SETTLE to maintain water geometry. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Have you checked the energy differences? Have you compared tpr files? Is the dispersion correction on and are you using some kind of shift/switch? (This has changed between 3.2 and 3.3). If you can not find the reason for this and it is reproducible then please submit a bugzilla with a 3.2.1 tpr file that reproduces the problem. Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re:Re:[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Hello, Thanks for your response. I have used the same tpr files for both the simulations. I compiled the tpr file in gromacs 3.2.1 and then used that tpr file to run simulations using the two versions of gromacs (i.e. only the mdrun was from different versions). I am not using any dispersion correction. There is also no switch or shift being used. I have pasted the run.mdp file below. The energies are different in the two cases. The LJ(SR) and the Coulomb are both different, resulting in different potential energies (PE) for the two. The PE of gromacs v3.3.1 is higher than that obtained by gromacs v3.2.1 (i.e v3.2.1 is more negative). In the pressure virials, I find that the diagonal terms are the same for the two versions (Vir-XX,YY and ZZ) however the off-diagonal are significantly different (magnitude of v3.2.1 v3.3.1),given below. Does this information give any indication as to what may be wrong? If not I will submit the tpr file to bugzilla. Thank you Sapna quantity gromacs v3.2.1 gromacs v3.3.1 Pressure (bar)0.5960180.838094 Vir-XX26640.5 26661.2 Vir-XY 6865.12 1.36518 Vir-XZ 6865.210.0121227 Vir-YX 6865.8 1.48257 Vir-YY 26652.3 26642.1 Vir-YZ 6886.45 3.93327 Vir-ZX 6861.23 -0.0529923 Vir-ZY 6882.24 3.87739 Vir-ZZ 2666526647.2 Run.mdp file: title = Water simulation ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step (ps) nsteps = 100 ; number of steps nstcomm = 1; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 100 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw= 1.0 ; cut-off for vdw rcoulomb = 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t= 0.5 ref_t = 300 Pcoupl = Berendsen Pcoupltype= isotropic; pressure geometry tau_p= 0.5 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; reference pressure gen_vel = yes ; generate initial velocities gen_temp = 300 ; initial temperature gen_seed = 2432384243 ; random seed Date: Tue, 18 Dec 2007 08:28:52 -0500 From: sapna sarupria [EMAIL PROTECTED] Subject: [gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1 To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Dear users, I had posted this question earlier too but did not get any response. I am re-posting it hoping someone can clarify this for me. I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (spc/e 10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I used SETTLE to maintain water geometry. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating
Re: [gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
sapna sarupria wrote: Hello, Thanks for your response. I have used the same tpr files for both the simulations. I compiled the tpr file in gromacs 3.2.1 and then used that tpr file to run simulations using the two versions of gromacs ( i.e. only the mdrun was from different versions). I am not using any dispersion correction. There is also no switch or shift being used. I have pasted the run.mdp file below. The energies are different in the two cases. The LJ(SR) and the Coulomb are both different, resulting in different potential energies (PE) for the two. The PE of gromacs v3.3.1 is higher than that obtained by gromacs v3.2.1 (i.e v3.2.1 is more negative). In the pressure virials, I find that the diagonal terms are the same for the two versions (Vir-XX,YY and ZZ) however the off-diagonal are significantly different (magnitude of v3.2.1 v3.3.1),given below. Does this information give any indication as to what may be wrong? If not I will submit the tpr file to bugzilla. Please submit a bugzilla. The off-diagonal terms in the virial should be small, which points to a possible error in 3.2.1 rather than 3.3.1. Have you compared the density with literature values? Thank you Sapna quantity gromacs v3.2.1 gromacs v3.3.1 Pressure (bar)0.5960180.838094 Vir-XX26640.5 26661.2 Vir-XY 6865.12 1.36518 Vir-XZ 6865.210.0121227 Vir-YX 6865.8 1.48257 Vir-YY 26652.3 26642.1 Vir-YZ 6886.45 3.93327 Vir-ZX 6861.23 -0.0529923 Vir-ZY 6882.24 3.87739 Vir-ZZ 2666526647.2 Run.mdp file: title = Water simulation ; a string cpp = /lib/cpp ; c-preprocessor dt = 0.002; time step (ps) nsteps = 100 ; number of steps nstcomm = 1; reset c.o.m. motion nstxout = 500 ; write coords nstvout = 500 ; write velocities nstlog = 100 ; print to logfile nstenergy = 500 ; print energies nstlist = 10 ; update pairlist ns_type= grid ; pairlist method coulombtype= PME rvdw= 1.0 ; cut-off for vdw rcoulomb = 1.0 ; cut-off for coulomb rlist = 1.0 ; cut-off for coulomb Tcoupl = Berendsen tc-grps = System tau_t= 0.5 ref_t = 300 Pcoupl = Berendsen Pcoupltype= isotropic; pressure geometry tau_p= 0.5 ; p-coupoling time compressibility = 4.5e-5 ; compressibility ref_p = 1.0 ; reference pressure gen_vel = yes ; generate initial velocities gen_temp = 300 ; initial temperature gen_seed = 2432384243 ; random seed Date: Tue, 18 Dec 2007 08:28:52 -0500 From: sapna sarupria [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Subject: [gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1 To: gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] Content-Type: text/plain; charset=iso-8859-1 Dear users, I had posted this question earlier too but did not get any response. I am re-posting it hoping someone can clarify this for me. I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (spc/e 10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I used SETTLE to maintain water geometry. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you
[gmx-users] Different system volumes from gromacs versions 3.2.1 and 3.3.1
Dear users, I performed NPT simulations of few different systems using both gromacs v3.2.1 and v3.3.1. I use exactly the same parameters, starting files, topology files etc for both the versions. The systems are pure water system (10684 water molecules) and a protein-water system. However, the average volume of the system that I get is from the simulations is different for the two versions. In case of pure water, gromacs v3.2.1 gives me a lower volume (~311.497 nm^3) than v3.3.1 (~324.604 nm^3) and the difference is significantly higher than the fluctuations in the volume. The pressure is maintained at 1 bar and the temperature is maintained at 300 K using Berendsen barostat and thermostat respectively. I was wondering if someone could tell me why this happens? Has there been a modification in the pressure virial calculation or something related to the same that leads to these differences? Thank you Regards Sapna -- Sapna Sarupria Ph.D. Student - Chemical Engineering Rensselaer Polytechnic Institute Troy, New York 12180 U.S.A. Ph#: (518)276-3031 Life isn't about finding yourself. Life is about creating yourself. George Bernard Shaw. Dare to Dream ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
