I have tried the same issue (same system with same mdp file and same initial configuration as starting structure) and is running without any problems with GROMACS-4.5.5.
Anyone knows what is happening? 2013/3/4, Justin Lemkul <jalem...@vt.edu>: > > > On 3/4/13 8:25 AM, Miguel Ángel Mompeán García wrote: >> 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. > > Bad idea. Nonbonded cutoffs are an intrinsic part of the force field. > Changing > them will actually increase your likelihood of failure. > >> 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? >> > > If EM stops at the first step, there's usually something catastrophically > wrong > with the starting configuration. If you've decreased the value of emstep, > there's little else that will account for such behavior. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 > -- 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
