Dear gmx users, I have successfully performed simulations on a charged peptide. I did a series of mutations and everything had a happy end. Now I have tried another mutation (just substitution of Asn to Lys) and I am getting the well-known
"X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group" message error during energy minimization, right at the beginning (step 0). My energy minimization mdp file looks as follows: integrator = steep ; emtol = 1000.0 ; emstep = 0.02 ; nsteps = 70000 ; nstlist = 1 ; ns_type = grid ; rlist = 1.0 ; coulombtype = PME ; rcoulomb = 1.0 ; rvdw = 1.0 ; pbc = xyz ; I have tried without neutralizing with ions, changing the time step, changing the integrator and the values for rcoulomb,rlist, etc. I have changed all the parameteres in the mdp file and I get a smaller value of particles in the message error, but still a crash. The box size has also no effect on the message error. I have checked the starting structure and everything is fine. Mutating that Asn to a non-charged residue does not yield any problem, but I want to study the effect in the Asn--> Lys mutation. Any hint to solve the error? -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
