[gmx-users] Is it possible to run implicit solvent simulations in parallel?

[Justin A. Lemkul]

Ozlem Ulucan wrote:
> Dear Justin,
> 
> Thanks for the fast response. The exact command I used is :
> 
> mdrun -v -s eq2.tpr -deffnm eq2 -g eq2.log -nice 19 >& eq2.out &
> 

This is for a serial run.  There's no problem with this (except that -s and -g 
are redundant with -deffnm, but that's not an issue).  What about your command 
for the parallel run?

-Justin

> Regards,
> 
> Ozlem
> 
> On Wed, May 4, 2011 at 3:23 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Ozlem Ulucan wrote:
> 
> 
>         Dear Gromacs Users,
> 
>         I have been trying to simulate a protein in implicit solvent.
>         When I used a single processor by setting -nt to 1 , I did not
>         encounter any problem.  But when I tried to run the simulations
>         using more than 1 processor I get the following error.
> 
>         Fatal error:
>         Constraint dependencies further away than next-neighbor
>         in particle decomposition. Constraint between atoms 2177--2179
>         evaluated
>         on node 3 and 3, but atom 2177 has connections within 4 bonds
>         (lincs_order)
>         of node 1, and atom 2179 has connections within 4 bonds of node 3.
>         Reduce the # nodes, lincs_order, or
>         try domain decomposition.
> 
>          I  set the lincs_order parameter in .mdp file to different
>         values. But it did not help.  I have some questions regarding
>         the information above.
> 
>          1) Is it possible to run implicit solvent simulations in parallel?
> 
> 
>     Yes.
> 
> 
>          2) As far as I know gromacs uses domain decomposition as
>         default. Why does in my simulations gromacs use the particle
>         decomposition which I do not ask for.
> 
> 
>     Without seeing the exact commands you gave, there is no plausible
>     explanation. DD is used by default.
> 
>     -Justin
> 
> 
>         Any suggestions are appreciated very much.
>          I am ussing gromacs-4.5.4 with charmm force field and the OBC
>         implicit solvent model. If you need further informations,
>         probably a run input file, let me know.
> 
>         Regards,
> 
>         Ozlem Ulucan
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     <tel:%28540%29%20231-9080>
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================