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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