Hi all, Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt?
Best, ---------- Forwarded message ---------- From: Juliette N. <[email protected]> Date: 1 April 2012 22:10 Subject: Re: [gmx-users] mdrun -rerun To: Discussion list for GROMACS users <[email protected]> On 1 April 2012 22:07, Mark Abraham <[email protected]> wrote: > On 2/04/2012 12:05 PM, Juliette N. wrote: >> >> 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 > > > If it even writes one, it will be identical to the -rerun file. There's no > way for the rerun code to get new configurations except by reading the input > trajectory. Thanks a lot :) > > Mark > > >>>> 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 >> >> >> > > -- > 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. -- 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
