On 1 April 2012 20:17, Mark Abraham <[email protected]> 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. > >Thank you Mark. I have a one component system. I guess group exclusions is >used for multicomponent systems where one needs to breakdown the total >energies.? In my case I need to exclude non bonded interaction of a polymer >chain with itself (avoid calculation of 1 and last atoms on chains if they >fall within cutoff radius) >> >> 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. > >I am a bit puzzled now. mdrun run takes on the old trajectory and recomputes >energies based on the old trajectory for each frame? If thats the case, then >use of nrexcel in order to obtain new trajectories fails I guess, as mdrun >rerun does not produce a new trajectory but only a new energy file?!
In other words, say I am doing NPT, with default nrexcel =3 I got a trajectory file and a density. Now with a new nrexcel that is large enough to exclude all nonbonded interactions of atoms on the same chain, I should expect a new trajectory and new density corresponding to this modified nrexcel. My concern is if what mdrun reruns does is just computing energies based on the old trajectory, I need to redo the simulations with a new top file (nrexcel=new number) because this new top file should affect the configuration. Am I right? So for instance, >> >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Thanks, J. N. -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
