On 2/04/2012 10:10 AM, Juliette N. wrote:
Hi all,
I have an enquiry regarding calculation of heat of vaporization by
estimating intermolecular nonbonded energies using mdrun rerun option.
mdrun -rerun should break the total nonbonded energy coming from
nonboded energy of (different molecules + a molecule with itself). By
setting appropriate nrexcl in top file I am trying to exclude
nonbonded part of molecule with itself within cut off radius so what
remains would be intermolecular nonbonded energy between different
molecules which determines heat of vaporization.
1) Is this approach correct?
For excluding a whole molecule, it could work. For excluding only a
part, using energy group exclusions (see manual) is more flexible. Just
setting energy groups suitably might work in your case, so that you get
the group-wise break-down of nonbonded energy.
2) If yes, can you please check the way I am applying mdrun rerun:
grompp -p nrexcl_3.top -o total_nonbonded.tpr
mdrun -deffnm total_nonbonded -s -o -c -g -e
I am done with these 5ns runs and now intend to exclude nonbonded
interaction on a chain by increasing nrexcl in top file named
nrexcl_new.top
grompp -p nrexcl_new.top -o new.tpr
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
2) Am I doing this correctly? I doubt because I provide -rerun
total_nonbonded.trr but dont know how to introduce -rerun
total_nonbonded.edr so that new energies get written on it?
You want to write new energies and keep the old ones in case you need
them. There's no reason to (want to) re-introduce the old ones. mdrun
-rerun accepts the trajectory to determine what configurations to
compute about. It doesn't need to know what some other algorithm thought
about the energies of that configuration.
3) If I want to re-calculate only the last 1 ns of runs (after system
is equilibrated), can I use -b 4000 ? i.e.:
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e
new -b 4000
Probably not. Check mdrun -h, but either way you can use trjconv first.
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
