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 4000 -- Thanks for your help, :) Best,
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