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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