Thanks On Fri, Mar 16, 2012 at 10:37 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 17/03/2012 12:39 AM, Anthony Cruz Balberdi wrote: > > > On Wed, Mar 14, 2012 at 8:42 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > >> On 15/03/2012 5:33 AM, Anthony Cruz Balberdi wrote: >> >>> Hi Users: >>> >>> I was trying to calculate the energy contribution of an specific ion in >>> my simulation. After extract a given frame from the simulation, I >>> recalculate the energies of this frame with mdrun -rerun. Then I used >>> tpbconv and editconf to create a new gro file and a new tpr without the >>> ion. I tried to run mdrun -rerun with this new files but the mdrun stops >>> with the following error: >>> >>> Program mdrun, VERSION 4.5.5 >>> Source code file: domdec_top.c, line: 744 >>> >>> Software inconsistency error: >>> Not enough position restraint coordinates >>> >>> What could be the problem? >>> >> >> Probably some [moleculetype] now has insufficient atoms to cope with >> its position restraints, which apparently weren't edited (correctly) by the >> tpbconv subset procedure. >> >> Any possible solution? >>> >> >> Probably depends on your use of position restraints, which would have >> been a good thing to have included in your original post.... > > > Thank for your answer and sorry for the missing information. The position > restraint is acting on the protein backbone. Since has nothing to do with > the ion, I dont understand why the error... > > Anthony > > > OK, so maybe tpbconv subsets don't work well with position restraints. You > can probably do what you want with a suitable combination of energy groups > and mdrun -rerun. > > Mark > > -- > 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
