2013/3/4 Justin Lemkul <jalem...@vt.edu> > Dear Justin, >
With 4.5.5 the jobs have completed. I am going to repeat them with 4.6.1 If you find something weird in the mdp file or require further explanations on the points do mention I will do my best to provide the necessary info. Right below are the comments: > In that case, it's probably something worth pursuing. Having the new > version fail when an older version works is curious. Can you please > provide all of the following details: > > 1. Compilers used to build Gromacs > 2. Hardware description These lines are from the CMakeOutput.log file: The system is: Linux - 2.6.32-5-amd64 - x86_64 (*****) Compiling the C compiler identification source file "CMakeCCompilerId.c" succeeded. Compiler: /usr/bin/gcc cc -v: gcc version 4.4.5 3. mdrun command > 4. Complete .mdp file grompp -f minimize.mdp -c Mut3.gro -o em.tpr -p topol.top mdrun -v -deffnm em The minimize.mdp file: integrator = steep emtol = 1000.0 emstep = 0.01 nsteps = 50000 nstlist = 1 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 pbc = xyz Thank-you a lot for all your tips and comments, Miguel > > > -Justin > > 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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> * Please search the archive at >>>>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at >>> http://www.gromacs.org/**Support/Mailing_Lists/Search<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<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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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