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. 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
