On 1 April 2012 20:17, Mark Abraham <mark.abra...@anu.edu.au> wrote: > 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
Hello all, I am a bit confused about whether or not mdp file has to be provided for grompp rerun step. In the original run (no mdrun I provide mdp as follows: grompp -f old.mdp -c old_em.gro -p nrexcl_3.top -o total_nonbonded.tpr (GROMPP old) then : mdrun -deffnm total_nonbonded -s -o -c -g -e Then I update the top file to new nrexcl= new value No do I have to provide the old mdp file and old gro file old_em.gro, which were used in (GROMPP old)? that is: (GROMPP new:) grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr mpirun –np 4 mdrun_mpi -rerun total_nonbonded.trr –deffnm new -s -o -c -g -e -x or I just have to use: grompp -p nrexcl_new.top -o new.tpr ( no -c and no -f flag) My other question is that the grompp with large nrexcl around 100 is taking a lot of time, while the default nrexcl=3 was grompp ed much faster. Why excluding bonds in this way is time consuming? Appreciate your comments, Best -- 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