On 7/1/16 8:36 AM, Faezeh Pousaneh wrote:
Thank you both, I am close to solve it. The remaining problem is when I
mdrun -rerun, it tells the number of atoms in old trajectory is not the
same as chosen index file.
Number of atoms in trajectory (24000) does not match the run input file
(16)
Your .tpr file needs to contain the same system that you ran before. The only
thing that changes is the energygrps setting in the .mdp file.
-Justin
can you help me?
Best regards
On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com>
wrote:
Hi,
Yes as Justin says, a group is a few molecules that you selected :-)
Mark
On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote:
On 7/1/16 7:55 AM, Faezeh Pousaneh wrote:
Thank you Mark, I see. But what is the solution then? The way you
proposed
''You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.''
is not my answer, since I do not want the energy for a ''group'' of
molecules, rather for specified combination of few molecules I define
from
g_select.
The only function available is to define energygrps in the .mdp file,
supply an
index file with those groups (e.g. from g_select) and do as Mark says and
re-calculate those interaction energies with mdrun -rerun on the existing
trajectory. The short-range nonbonded interaction energies between those
groups
will be written to their own terms in a new .edr file.
-Justin
Best regards
On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <
mark.j.abra...@gmail.com>
wrote:
Hi,
The .edr file contains only what was written during the simulation,
and
that was for any energy groups defined before that run. You're trying
to
ask it to make an arbitrary repartition, which it can't do unless it
recorded every component of the energy for every frame (which would
take
forever and use lots of disk). You can make a new .tpr file with those
energy groups and use mdrun -rerun on the old trajectory, however.
Mark
On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosa...@gmail.com>
wrote:
Hi
Does someone know how to obtain energy between specific molecules in
the
system?
What I did and seems not be correct is:
1- I obtained the molecules I wanted to look at:
g_select_mpi -f 600gro.gro -s production.tpr -on
2- Then I produced a .tpr file for the chosen selection,index.ndx,
tpbconv -s production.tpr -n index.ndx -o tpxout.tpr
3- Finally put the created .tpr file as an input for g_energy
g_energy -f ener.edr -s tpxout.tpr (either, g_energy -s tpxout.tpr)
But that is not the solution, since it gives energy for whole system.
Best regards
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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