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).
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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