[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4
Berk Hess
gmx3 at hotmail.com
Wed Feb 4 09:03:29 CET 2009
Hi,
I always get confused by the atom names in TIP4P.
But MW is not a mass, but the vsite, right?
Velocities of vsites are completely irrelevant, except if you would want to analyze them.
I might have changed something to the initial velocities of vsites for 4.0.
I would guess that 4.0 has the correct initial vsite velocities,
but I would have to check to be sure.
Again, velocities of vsites do are completely irrelevant for anything,
except printing them in the output.
Berk
> Date: Wed, 4 Feb 2009 08:25:35 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4
>
> Chris Neale wrote:
> > contrary to my previous stament, I am no longer convinced that it is
> > simply an initial constraints issue.
>
> There are two things to do:
> 1. run gmx3.3 and gmx4.0 with the 3.3 tpr file. This should give the
> same result in principle.
> 2. run gmx3.3 and gmx4.0 with their own tpr files. Here you can use
> gmxcheck -s1 -s2 to compare the files.
>
> The differences due to initial constraints are small usually, but they
> seem comparable in your case. Defining flexible should remove all
> difference due to constraints (unless constraints are turned on in the
> mdp file which selects LINCS over the default SETTLE).
>
> Anyway it is important to distinguish the apples from the oranges, hence
> point 1 is the best to test it. Obviously you are aware that the MW
> velocity does not in anyway influence the energy or the dynamics, since
> it merely shows the displacement of the particle divided by the time
> step. Therefore it would be good to compare energies as well from a 3.3
> run and a 4.0 run.
>
> >
> > In my last post, I stated: "when I define -DFLEXIBLE and make the tpr
> > using gromacs 3 and then run using gromacs 4, I do get gromacs 4 -
> > identical velocities.". However, thinking more on this has me believing
> > that this only indicates that the difference occurs at the mdrun stage.
> >
> > I did a few more tests to see what the difference was when turning on or
> > off the unconstrained start option
> > in either gromacs 3 or gromacs 4. I see a very small diffence in
> > velocities compared to the MW difference between
> > gromacs 3 or gromacs 4 mdruns.
> >
> > Below showing gromacs 4, using unconstrained_start=no vs.
> > unconstrained_start=yes has differences, but very minor.
> >
> > diff gmx4.0.3_noUCS/feoff.gro gmx4.0.3/feoff.gro ...
> > < 51SOL OW 1151 6.816 4.071 1.558 0.0549 0.4777 -0.4315
> > < 51SOL HW1 1152 6.851 4.082 1.470 -0.1304 0.6992 -0.4795
> > < 51SOL HW2 1153 6.727 4.106 1.553 -0.2840 -0.3333 -0.3852
> > < 52SOL OW 1155 3.564 2.550 1.079 0.0951 0.0648 0.1748
> > < 52SOL HW1 1156 3.521 2.598 1.009 1.5023 0.4847 -0.4757
> > < 52SOL HW2 1157 3.551 2.604 1.157 0.0156 0.5140 -0.1424
> > ---
> >> 51SOL OW 1151 6.816 4.071 1.558 0.0554 0.4775 -0.4315
> >> 51SOL HW1 1152 6.851 4.082 1.470 -0.1306 0.6992 -0.4793
> >> 51SOL HW2 1153 6.727 4.106 1.553 -0.2903 -0.3308 -0.3857
> >> 52SOL OW 1155 3.564 2.550 1.079 0.0951 0.0648 0.1747
> >> 52SOL HW1 1156 3.521 2.598 1.009 1.5034 0.4843 -0.4719
> >> 52SOL HW2 1157 3.551 2.604 1.157 0.0147 0.5151 -0.1438
> > ...
> >
> > with some, but not all MW showing small differences:
> > < 54SOL OW 1163 5.835 7.123 3.589 -0.0214 -0.1603 0.5173
> > < 54SOL HW1 1164 5.788 7.068 3.651 0.4698 -0.5196 0.5833
> > < 54SOL HW2 1165 5.841 7.208 3.632 -0.8849 -0.0052 0.3674
> > < 54SOL MW 1166 5.830 7.127 3.602 -0.0578 -0.2071 0.4856
> > ---
> >> 54SOL OW 1163 5.835 7.123 3.589 -0.0214 -0.1604 0.5172
> >> 54SOL HW1 1164 5.788 7.068 3.651 0.4694 -0.5205 0.5835
> >> 54SOL HW2 1165 5.841 7.208 3.632 -0.8844 -0.0018 0.3686
> >> 54SOL MW 1166 5.829 7.127 3.602 -0.0578 -0.2071 0.4856
> >
> >
> > Below showing gromacs 3, using unconstrained_start=no vs.
> > unconstrained_start=yes has differences, but very minor.
> >
> > diff gmx3.3.1_noUCS/feoff.gro gmx3.3.1/feoff.gro ...
> > < 51SOL OW 1151 6.816 4.071 1.558 0.0550 0.4778 -0.4315
> > < 51SOL HW1 1152 6.851 4.082 1.470 -0.1304 0.6992 -0.4795
> > < 51SOL HW2 1153 6.727 4.106 1.553 -0.2841 -0.3333 -0.3852
> > < 51SOL MW 1154 6.809 4.077 1.546 0.0254 -0.0273 0.0172
> > < 52SOL OW 1155 3.564 2.550 1.079 0.0951 0.0648 0.1749
> > < 52SOL HW1 1156 3.521 2.598 1.009 1.5023 0.4846 -0.4757
> > < 52SOL HW2 1157 3.551 2.604 1.157 0.0157 0.5140 -0.1425
> > < 52SOL MW 1158 3.557 2.563 1.080 -0.0486 0.0225 -0.0022
> > ---
> >> 51SOL OW 1151 6.816 4.071 1.558 0.0554 0.4775 -0.4315
> >> 51SOL HW1 1152 6.851 4.082 1.470 -0.1306 0.6992 -0.4793
> >> 51SOL HW2 1153 6.727 4.106 1.553 -0.2903 -0.3308 -0.3857
> >> 51SOL MW 1154 6.809 4.077 1.546 0.0219 -0.0279 0.0237
> >> 52SOL OW 1155 3.564 2.550 1.079 0.0951 0.0648 0.1747
> >> 52SOL HW1 1156 3.521 2.598 1.009 1.5034 0.4843 -0.4719
> >> 52SOL HW2 1157 3.551 2.604 1.157 0.0147 0.5151 -0.1438
> >> 52SOL MW 1158 3.557 2.563 1.080 -0.0421 0.0144 0.0060
> >
> > ...
> >
> > < 54SOL OW 1163 5.835 7.123 3.589 -0.0215 -0.1603 0.5173
> > < 54SOL HW1 1164 5.788 7.068 3.651 0.4698 -0.5196 0.5834
> > < 54SOL HW2 1165 5.841 7.208 3.632 -0.8849 -0.0051 0.3674
> > < 54SOL MW 1166 5.830 7.127 3.602 0.1837 -0.0398 0.1193
> > ---
> >> 54SOL OW 1163 5.835 7.123 3.589 -0.0214 -0.1604 0.5172
> >> 54SOL HW1 1164 5.788 7.068 3.651 0.4694 -0.5205 0.5835
> >> 54SOL HW2 1165 5.841 7.208 3.632 -0.8844 -0.0018 0.3686
> >> 54SOL MW 1166 5.830 7.127 3.602 0.1879 -0.0399 0.1103
> > ...
> >
> > In the above cases, other specified .mdp options were:
> >
> > integrator = md
> > comm_mode = linear
> > nstcomm = 1
> > comm_grps = System
> > nstlist = 5
> > ns_type = grid
> > pbc = xyz
> > coulombtype = PME
> > rcoulomb = 0.9
> > fourierspacing = 0.12
> > pme_order = 4
> > vdwtype = cut-off
> > rvdw_switch = 0
> > rvdw = 1.4
> > rlist = 0.9
> > constraints = none
> > energygrps = System
> > nsteps = 0
> > dt = 0.004
> > gen_vel = no
> > unconstrained-start = <yes or no depending on the test>
> >
> > ######
> >
> > And note that if I set
> > constraints = all-bonds
> > constraint_algorithm= lincs
> > lincs-iter = 1
> > lincs-order = 6
> >
> > then the difference between unconstrained-start=yes or =no was similarly
> > small.
> >
> > Therefore it seems to me that something other than initial constraints
> > is leading to this difference.
> >
> > Chris.
> >
> > -- original message --
> >
> > Thanks David, you are correct about initial step constraints. More
> > information inline below, but my question has been resolved.
> >
> > >Chris Neale wrote:
> > >> Hello,
> > >>
> > >> Does anybody know if there is a reason why the .gro output velocities
> > >> would be different for tip4p MW in a zero-step mdrun between gromacs 3
> > >> and gromacs 4 (3.3.1 and 3.3.3 are the same, and are different from
> > >> 4.0.2 and 4.0.3, which are themselves the same).
> > >Is this with the same tpr?
> >
> > This was utilizing a tpr generated by the same version of gromacs as was
> > used from the mdrun (3.3.1 grompp for 3.3.1 mdrun, etc.) although the
> > input was identical (with the exception of any undefined .mdp options
> > whose default values changes between v3 and v4, although I can't think
> > of one that affects only MW).
> >
> > Based on your question, I did redo the 3.3.1 grompp to generate a single
> > .tpr that was used for both 3.3.1 mdrun and 4.0.3 mdrun. The results are
> > the same:
> >
> > $ diff 4.gro 3.gro | head
> > 1156c1156
> > < 51SOL MW 1154 6.809 4.077 1.546 0.0120 0.3740 -0.4572
> > ---
> > > 51SOL MW 1154 6.809 4.077 1.546 0.0219 -0.0279 0.0237
> > 1160c1160
> > < 52SOL MW 1158 3.557 2.563 1.080 0.2917 0.2007 0.0277
> > ---
> > > 52SOL MW 1158 3.557 2.563 1.080 -0.0421 0.0144 0.0060
> >
> > >
> > >It could have to do with initial step constraints.
> >
> > I had considered that, but my .mdp uses unconstrained-start = yes.
> >
> > Based on your suggestion I have attempted setting:
> > 1. constraints = none (get the same difference)
> > 2. also define = -DFLEXIBLE (get the same difference)
> >
> > However, when I define -DFLEXIBLE and make the tpr using gromacs 3 and
> > then run using gromacs 4
> > I do get gromacs 4 - identical velocities.
> >
> > $ diff 4from3.gro 4.gro | head
> > $ diff 4from3.gro 3.gro | head
> > 1156c1156
> > < 51SOL MW 1154 6.809 4.077 1.546 0.0120 0.3740 -0.4572
> > ---
> > > 51SOL MW 1154 6.809 4.077 1.546 0.0219 -0.0279 0.0237
> > 1160c1160
> > < 52SOL MW 1158 3.557 2.563 1.080 0.2917 0.2007 0.0277
> > ---
> > > 52SOL MW 1158 3.557 2.563 1.080 -0.0421 0.0144 0.0060
> > 1164c1164
> > < 53SOL MW 1162 2.458 4.404 3.060 -0.0763 0.0165 -0.5712
> >
> > So thank you, this explains it.
> >
> > Chris.
> >
> > >>
> > >> diff gmx4.0.3/feoff.gro gmx3.3.1/feoff.gro | head
> > >> 1156c1156
> > >> < 51SOL MW 1154 6.809 4.077 1.546 0.0120 0.3740 -0.4572
> > >> ---
> > >> > 51SOL MW 1154 6.809 4.077 1.546 0.0219 -0.0279 0.0237
> > >> 1160c1160
> > >> < 52SOL MW 1158 3.557 2.563 1.080 0.2917 0.2007 0.0277
> > >> ---
> > >> > 52SOL MW 1158 3.557 2.563 1.080 -0.0421 0.0144 0.0060
> > >> ...
> > >> (continues for all MW)
> > >>
> > >> This difference does not appear to be related to solvent optimization:
> > >>
> > >> $ diff gmx4.0.3/feoff.gro gmx4.0.3_GMX_NO_SOLV_OPT/feoff.gro
> > >>
> > >> I might just chalk this up to different mdp option defaults, but it
> > >> seems strange that there is a difference for all MW, but not for any
> > >> other atoms in the system.
> > >>
> > >> $ cat dpc50_md11.mdp
> > >> integrator = md
> > >> comm_mode = linear
> > >> nstcomm = 1
> > >> comm_grps = System
> > >> nstlist = 5
> > >> ns_type = grid
> > >> pbc = xyz
> > >> coulombtype = PME
> > >> rcoulomb = 0.9
> > >> fourierspacing = 0.12
> > >> pme_order = 4
> > >> vdwtype = cut-off
> > >> rvdw_switch = 0
> > >> rvdw = 1.4
> > >> rlist = 0.9
> > >> constraints = all-bonds
> > >> constraint_algorithm= lincs
> > >> lincs-iter = 1
> > >> lincs-order = 6
> > >> energygrps = System
> > >> nsteps = 0
> > >> dt = 0.004
> > >> gen_vel = no
> > >> unconstrained-start = yes
> > >>
> > >> Note that I explicitly included the tip4p.itp from gromacs 3.3.1 in
> > both
> > >> runs.
> > >>
> > >> Perhaps this is related to the gromacs 3 vsite problem?
> > >> http://www.gromacs.org/pipermail/gmx-users/2008-November/037659.html
> > >>
> > >> Thanks,
> > >> Chris.
> >
> > _______________________________________________
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>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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