----- Original Message ----- From: Nilesh Dhumal <ndhu...@andrew.cmu.edu> Date: Wednesday, October 27, 2010 1:04 Subject: Re: [gmx-users] (no subject) To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> I used the same .tpr file. I added -dlb yes and - > reprod yes during mdrun > with rerun option. Still I am not geting why energy, temp, > pressure are > changing since I have same topology file and .trr file. As I said last time, a parallel rerun cannot reproduce a run unless they're both run under the same conditions. Changing the options for the rerun cannot achieve this, because the original run probably had dynamic load balancing. Mark > Is there any bug in rerun option? > Nilesh > > On Mon, October 25, 2010 8:50 pm, Mark Abraham wrote: > > > > > > > ----- Original Message ----- > > From: Nilesh Dhumal <ndhu...@andrew.cmu.edu> > > Date: Tuesday, October 26, 2010 10:50 > > Subject: Re: [gmx-users] (no subject) > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > > > > >> I run a test simulation for -rerun. I didn't change the > topology file. > >> > >> > >> grompp -f md.mdp -c solvent-bmi-pf6-128.pdb > - p > >> solvent-bmi-pf6-128.top -o 3.tpr > >> mpirun -machinefile cp -np 8 mdrun -s 3.tpr -o 3.trr -c > >> solvent-bmi-pf6-128.pdb -e 3.edr -g 3.log > >> > >> with -rerun grompp -f md.mdp -c solvent-bmi-pf6- > 128.pdb - p > >> solvent-bmi-pf6-128.top -o 6.tpr > >> mpirun -machinefile cp -np 8 mdrun -s 6.tpr -o 6.trr -rerun > 3.trr -c > >> solvent-bmi-pf6-128.pdb -e 6.edr -g 6.log > >> > >> I calculate the total energy by > >> g_energy -f 3.edr -o 3.xvg g_energy -f 6.edr -o 6.xvg > >> > >> The total energy varies between +- 30.00 KJ/mol. > >> It should be constant since I using same topology file and > trajectory.>> Why the total energy is not constant. > >> > > > > Those .tpr should be identical - but you can check that with > gmxcheck.> Reruns do neighbour-searching every step, whereas > your normal simulation > > followed the nstlist setting. That's part of why my earlier advice > > suggested doing reruns for each simulation you wish to > compare. You > > should be able to get good/better agreement for steps where nstlist > > directed neighbour-searching in the original run. Also, > whether or not > > constraints have been applied (and when!) could influence the > energies to > > about this degree. I don't recall the details here. > > > > Even once you've removed all algorithm-specific sources of > difference,> there are other sources of non-reproducibility, > such as the assignment of > > particles to DD cells. Your original mdrun probably used dynamic > > load-balancing, and that cannot be reproduced in the DD used > by the > > rerun. (Or indeed by a repeat of your original mdrun!) Setting > -dlb no in > > the original simulation might be enough to get agreement here, > or maybe > > mdrun -reprod will be required. > > > > Mark > > > > > >> NIlesh > >> > >> > >> > >> > >> > >> On Thu, October 21, 2010 10:24 am, Mark Abraham wrote: > >> > >>> On 22/10/2010 1:17 AM, Nilesh Dhumal wrote: > >>> > >>> > >>>> I am doing solvation dynamics for my system. > >>>> I have system with diatomic (PA---NE)solute surrounded by water > >>>> molecules. > >>>> > >>>> I want to run simulation with two differcent cases. > >>>> 1. PA charge=0 and NE charge=0 : No charge on solute > >>>> 2. PA charge=+1 and NE charge=-1 : Charge on solute > >>>> > >>>> > >>>> > >>>> I want to calculate the energy at each step keeping the solvent > >>>> configration same. > >>>> > >>>> IF I start a simulation with no charge on solute (case1), I > >>>> > >> have the > >>>> energy for 1 step. I want to calculate the energy with charge > >> on solute > >>>> (case 2) with same configration water molecules. > >>>> Each step I want to calculate the energy with and > >>>> > >> without charge on > >>>> solute since the configration of solvent will be same for > >> that step. > >>>> > >>>> I was thinking two make two topologies file with charge and > >>>> > >> with out > >>>> charge on solute. I don't know how to use them simultaneously > >> during the > >>>> simulation. > >>> > >>> Well, you don't use them simultaneously. You run a > simulation on > >>> whatever you think will generate a relevant conformational > >> ensemble. Then > >>> you want to use mdrun -rerun twice on the resulting > >> trajectory, using .tpr > >>> files based on .top files corresponding to the two cases in > >> order to > >>> create your comparison. > >>> > >>> Mark > >>> -- > >>> 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 > >>> > >>> > >>> > >>> > >> > >> > >> > >> -- > >> 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 > >> > > -- > > 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 > > > -- > 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
-- 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
