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

[Ozlem Ulucan]

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 &

Regards,

Ozlem

On Wed, May 4, 2011 at 3:23 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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