Thanks. One last question. So whats the new trr file provided by -o flag of mdrun rerun below?
mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new >> 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? > > > Yes, per mdrun -h. > > >>> 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? > > > If you want new configurations based on some Frankenstein of your model > physics, then you do not need mdrun -rerun. > > Mark > > >> >> 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 >> >> >> > > -- > 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
