[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.
> Ozlem Ulucan
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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