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
<mailto: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
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