Re: [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!
Dear Mark, users and developers... Indeed, the source of the problems comes from both the constraints and the pressure bath. The temperature bath did not seem to interfere. Now, the problem is clear, to remove constraints is not only compulsory but also recommendable for such simulations. However, the pressure bath (which is the major source of the problems) should not play such a role. This is a limitation of the current implementation of GROMACS or just a plain BUG. I think most people would agree that one should not be limited to NVT simulations when using freeze groups. A previous version (3.2.1) that we have been using in our group was completely immune to both pressure bath and constraints when simulating a frozen protein in water. As far as I remember, this older version did a normal step integration with all its requisites and, in the end, just took back the previous positions for the frozen group (protein). My question remains... Will we be able to use freeze groups together with a NPT simulation in Gromacs 4.5.x??? Any comments from the developers are welcome... Regards, Miguel On 11/11/2010 1:07 AM, Mark Abraham wrote: On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote: Dear users and developers, In GROMACS 4.5.x when using "freeze groups" on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, this is wrong! Are there any options in MDP/GROMPP/MDRUN that can be originating this? Or it is some bug in the code? A copy of my input file follows below. Note that this version of GROMACS crashes if one uses "constraints" in LINCS together with "freeze groups". Hence the "constraints = none" line. Indeed, because imposing the constraints can perturb the (frozen) positions slightly, leading to numerical issues... Similarly, if you couple the frozen groups to a heat bath, you're going to find that they're not actually frozen. And pressure-coupling is not known to always play nicely with frozen groups either (search the archive for more). Any help is appreciated. Regards, Miguel _ ; Input file ; title = zzz cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002; ps ! nsteps = 100 nstcomm = 10 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstenergy = 500 nstcalcenergy = 10 ns_type = grid coulombtype = Generalized-Reaction-Field nstlist = 5 rlist = 0.8 rcoulomb= 1.4 epsilon_rf = 54.0 rvdw= 1.4 vdwtype = cut-off ; Energy monitoring energygrps = Protein SOL Tcoupl = v-rescale tc-grps = Protein SOL tau_t = 0.10 0.10 ref_t = 310.0 310.0 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; lincs_order value of 8 works better than 4 constraint_algorithm=lincs lincs_order = 8 constraints = none lincs-warnangle = 90 freezegrps = Protein freezedim = Y Y Y energygrp_excl = Protein Protein -- Miguel Machuqueiro Department of Chemistry and Biochemistry Faculty of Sciences, University of Lisbon Campo Grande, Edifício C8 (sala 8.5.47) 1149-016 Lisboa, Portugal Tel. : +351 217500112 (int.ext.28547) Mobile: +351 967562285 E-mail: machuque at fc.ul.pt www1: http://webpages.fc.ul.pt/~mamachuqueiro www2: http://cqb.fc.ul.pt/intheochem __ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!
On 11/11/2010 3:14 AM, Miguel Machuqueiro wrote: Dear users and developers, In GROMACS 4.5.x when using "freeze groups" on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, this is wrong! Are there any options in MDP/GROMPP/MDRUN that can be originating this? Or it is some bug in the code? A copy of my input file follows below. Note that this version of GROMACS crashes if one uses "constraints" in LINCS together with "freeze groups". Hence the "constraints = none" line. Indeed, because imposing the constraints can perturb the (frozen) positions slightly, leading to numerical issues... Similarly, if you couple the frozen groups to a heat bath, you're going to find that they're not actually frozen. And pressure-coupling is not known to always play nicely with frozen groups either (search the archive for more). Any help is appreciated. Regards, Miguel _ ; Input file ; title = zzz cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002; ps ! nsteps = 100 nstcomm = 10 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstenergy = 500 nstcalcenergy = 10 ns_type = grid coulombtype = Generalized-Reaction-Field nstlist = 5 rlist = 0.8 rcoulomb= 1.4 epsilon_rf = 54.0 rvdw= 1.4 vdwtype = cut-off ; Energy monitoring energygrps = Protein SOL Tcoupl = v-rescale tc-grps = Protein SOL tau_t = 0.10 0.10 ref_t = 310.0 310.0 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; lincs_order value of 8 works better than 4 constraint_algorithm=lincs lincs_order = 8 constraints = none lincs-warnangle = 90 freezegrps = Protein freezedim = Y Y Y energygrp_excl = Protein Protein -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Freeze Groups in Gromacs 4.5.x (bug?)!!!
Dear users and developers, In GROMACS 4.5.x when using "freeze groups" on a Protein in a Protein+Solvent system, I noticed that the coordinates of a few atoms (not many, but a few) are changed after a short period of MD (~0.2 ps). Of course, this is wrong! Are there any options in MDP/GROMPP/MDRUN that can be originating this? Or it is some bug in the code? A copy of my input file follows below. Note that this version of GROMACS crashes if one uses "constraints" in LINCS together with "freeze groups". Hence the "constraints = none" line. Any help is appreciated. Regards, Miguel _ ; Input file ; title = zzz cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002; ps ! nsteps = 100 nstcomm = 10 nstxtcout = 500 xtc-precision = 1000 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 0 nstenergy = 500 nstcalcenergy = 10 ns_type = grid coulombtype = Generalized-Reaction-Field nstlist = 5 rlist = 0.8 rcoulomb= 1.4 epsilon_rf = 54.0 rvdw= 1.4 vdwtype = cut-off ; Energy monitoring energygrps = Protein SOL Tcoupl = v-rescale tc-grps = Protein SOL tau_t = 0.10 0.10 ref_t = 310.0 310.0 ; Isotropic pressure coupling is now on Pcoupl = berendsen Pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; lincs_order value of 8 works better than 4 constraint_algorithm=lincs lincs_order = 8 constraints = none lincs-warnangle = 90 freezegrps = Protein freezedim = Y Y Y energygrp_excl = Protein Protein -- Miguel Machuqueiro Department of Chemistry and Biochemistry Faculty of Sciences, University of Lisbon Campo Grande, Edifício C8 (sala 8.5.47) 1149-016 Lisboa, Portugal Tel. : +351 217500112 (int.ext.28547) Mobile: +351 967562285 E-mail: machuque at fc.ul.pt www1: http://webpages.fc.ul.pt/~mamachuqueiro www2: http://cqb.fc.ul.pt/intheochem __ -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
