[gmx-users] is the tip4p MW velocity treated differently in gromacs 3 vs 4

[Chris Neale]

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.