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

Justin A. Lemkul jalemkul at vt.edu
Wed May 4 15:23:06 CEST 2011

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?


>  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.


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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