[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4
David van der Spoel
spoel at xray.bmc.uu.se
Tue Feb 3 22:21:04 CET 2009
Chris Neale wrote:
> 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?
It could have to do with initial step constraints.
> diff gmx4.0.3/feoff.gro gmx3.3.1/feoff.gro | head
> < 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
> < 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
> Perhaps this is related to the gromacs 3 vsite problem?
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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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