[gmx-users] Is it possible to run implicit solvent simulations in parallel?
ulucan.oz at googlemail.com
Wed May 4 15:17:12 CEST 2011
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
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
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.
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