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

[Ozlem Ulucan]

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.

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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