[gmx-users] mdrun -rerun

Juliette N. joojoojooon at gmail.com
Mon Apr 2 02:10:29 CEST 2012

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?

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?

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

Thanks for your help, :)
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