[gmx-developers] mdrun -membed not functional with pieces > 1 ?

Jochen Hub jhub at gwdg.de
Thu Jul 30 14:07:06 CEST 2015


I am trying to put two molecules into a membrane with mdrun -membed.
This should be possible with the option pieces = 2 in membed.dat.
However, when mdrun checks if the energy group exclusions are consistent
with the group chosen, one gets something like:

Energy exclusions "mol1" and  "mol1" do not match the group to embed "mol0"

The problem seems the check pasted below. It works only if there is an
exclusion only between the atoms of *one* group (such as "Protein
Protein"), but not with two groups (such as "mol0 mol0 mol1 mol1".
However, if one makes one large group containing all pieces (here mol0
and mol1), then a consistency check with the freezegroups fails.

Do I miss something here? Did anyone get mdrun -membed working with
pieces > 1 ?

Many thanks,

for (i = 0; i < ng; i++)
   for (j = 0; j < ng; j++)
     if (inputrec->opts.egp_flags[ng*i+j] == EGP_EXCL)
       bExcl = TRUE;
       if ( (groups->grps[egcENER].nm_ind[i] != ins_grp_id) ||
            (groups->grps[egcENER].nm_ind[j] != ins_grp_id) )
          gmx_fatal(FARGS, "Energy exclusions \"%s\" and  \"%s\" do not
match the group "
                                  "to embed \"%s\"",
*groups->grpname[groups->grps[egcENER].nm_ind[j]], ins);

Dr. Jochen Hub
Computational Molecular Biophysics Group
Institute for Microbiology and Genetics
Georg-August-University of Göttingen
Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.
Phone: +49-551-39-14189

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