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

[David van der Spoel]

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?

It could have to do with initial step constraints.
> 
> 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.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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