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

[Justin A. Lemkul]

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
> 

-- 
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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

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