[gmx-users] mdrun -rerun

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 2 02:17:43 CEST 2012

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.


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