The version I was using this morning was 4.6
2013/3/4, Justin Lemkul <jalem...@vt.edu>: > > > On 3/4/13 3:08 PM, Miguel Ángel Mompeán García wrote: >> 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? >> > > You didn't tell us your Gromacs version in the previous post so the best > guess > is "random bug that was somehow fixed before 4.5.5." > > -Justin > >> >> 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 >>> > > -- > ======================================== > > 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
