Well … 400 ps is rather small and you can expect deviations from so short simulations if you start from an non-equilibrated system. I am not sure what the void is but this indicates that your system might not be equilibrated …
You can try to decrease the time step and nstlist to see if you the drop of temperature is due a flow of energy. On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 <stephane.a...@cea.fr> wrote: > Hello Xavier, > > Thank you for your response. > >>> nstlist = 10 and the rlist = 1.0 > My mistake, i did not changes these values when i switched to PME, > > I have rerun the simulations for 400 ps in NPT with these changes and plotted > Epot and Temp vs Time The Epot and Temp values are not stables. The average > Temp of the system is better than previously but fluctuate around (294 K) > instead of 298 K . Note i use gmx4.5.5 to do my calculations. > > I have also visualized my system at the end of the NPT run, the na+, water, > surfactant, octane molecules form a slab with void > > What's wrong ? > > Stephane > > > > ------------------------------ > > Message: 5 > Date: Thu, 25 Apr 2013 13:34:21 +0200 > From: XAvier Periole <x.peri...@rug.nl> > Subject: Re: [gmx-users] Martini with PME, temp two low > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <4632c83b-cd6f-4c92-b887-a1c39dff4...@rug.nl> > Content-Type: text/plain; charset=us-ascii > > > Did you visualise the system? T in function of time? Epot in function of time? > > As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = > 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 > if nstlist =10. > > On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 <stephane.a...@cea.fr> > wrote: > >> Hello all, >> >> I am trying to test the martini force field with PME for a charged system >> that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. >> My system works well, if i use the standard shift parameters (correct temp, >> and pressure). But for for the simulation with PME , the temp of the system >> decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K >> >> >> integrator = md >> dt = 0.020 >> nsteps = 10000 ; 200ps >> nstcomm = 10 >> comm-grps = >> ;refcoord_scaling = com >> >> nstxout = 0 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstenergy = 100 >> ;nstxtcout = 1000 >> xtc_precision = 100 >> ;xtc-grps = >> energygrps = AOT W ION OCT >> >> nstlist = 10 >> ns_type = grid >> pbc = xyz >> rlist = 1. >> >> ; PME parameters >> coulombtype = PME >> rcoulomb = 1.2 >> rvdw = 1.2 >> fourierspacing = 0.12 >> fourier_nx = 0 >> fourier_ny = 0 >> fourier_nz = 0 >> pme_order = 4 >> >> tcoupl = v-rescale >> tc-grps = AOT_W_ION OCT >> tau_t = 1.0 1.0 >> ref_t = 298 298 >> Pcoupl = berendsen >> Pcoupltype = isotropic >> tau_p = 1.0 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> >> ;gen_vel = no >> ;gen_temp = 0 >> ;gen_seed = 473529 >> >> >> ; MARTINI and CONSTRAINTS >> ; for ring systems and stiff bonds constraints are defined >> ; which are best handled using Lincs. >> >> constraints = none >> constraint_algorithm = Lincs >> unconstrained_start = no >> lincs_order = 4 >> lincs_warnangle = 3 >> >> >> Results obtained with W/ PME >> >> Statistics over 10001 steps using 1001 frames >> >> Energies (kJ/mol) >> Bond G96Angle LJ (SR) Coulomb (SR) Coul. recip. >> 1.63789e+04 1.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04 >> Potential Kinetic En. Total Energy Temperature Pressure (bar) >> -4.41367e+05 7.81801e+04 -3.63187e+05 2.90373e+02 -1.76470e+01 >> T-AOT_W_ION T-OCT >> 2.90629e+02 2.90357e+02 >> >> Results W:o PME >> >> Energies (kJ/mol) >> Bond G96Angle LJ (SR) Coulomb (SR) Potential >> 1.60482e+04 1.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05 >> Kinetic En. Total Energy Temperature Pressure (bar) >> 8.02685e+04 -2.37777e+05 2.98129e+02 -3.07123e+01 >> >> Box-X Box-Y Box-Z >> 1.52926e+01 1.52926e+01 1.52926e+01 >> >> >> T-AOT_W_ION T-OCT >> 2.98141e+02 2.98129e+02 >> >> >> Did I miss something ? >> >> >> Note that for the moment i do not use the polarizable water model. >> >> Thanks for your help >> >> Stephane >> >> >> >> >> -- >> 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 > > > > ------------------------------ > > Message: 6 > Date: Thu, 25 Apr 2013 14:05:51 +0200 > From: Berk Hess <g...@hotmail.com> > Subject: RE: [gmx-users] Differences between 4.5.5 and 4.6.2-dev? > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <dub124-w4fd05b41f4efbf070fdd08e...@phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Twin-range will lead to extra errors, which could be negligible or not. > But the errors should be the same and have the same effects in different > versions. > I think nothing has changed in the twin-range treatment from 4.5 to 4.6, but > I am not 100% sure. > > Which version with twin-range matches your non twin-range results? > > Cheers, > > Berk > > ---------------------------------------- >> Subject: Re: [gmx-users] Differences between 4.5.5 and 4.6.2-dev? >> From: kes...@icp.uni-stuttgart.de >> Date: Thu, 25 Apr 2013 10:38:35 +0200 >> To: gmx-users@gromacs.org >> >> Dear Berk, der GMXers, >> >> On Apr 23, 2013, at 2:54 PM, Stefan Kesselheim <kes...@icp.uni-stuttgart.de> >> wrote: >> >>> The temperature is 300.6, target temperature was 300. That should be fine. >>> I did check weaker fields and weaker thermostat coupling. Everything stayed >>> optimally consistent, within 4.5.5, however incompatible with 4.6.2. >>> I'm rerunning with cutoffs=1.4 now. I should get results by tomorrow. >> >> Now results are there and without twin-range I obtain consistent results >> between the GMX-versions. I'm now switching on twin-range and rerunning to >> check if the error does reappear. >> >> I don't know what would be better: Either I did something wrong in a very >> stupid way, or ... >> >> Thanks for your patience >> Stefan >> >> -- >> 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 > > ------------------------------ > > Message: 7 > Date: Thu, 25 Apr 2013 14:28:56 +0200 > From: Sainitin Donakonda <saigr...@gmail.com> > Subject: [gmx-users] Problem with gromacs in Cluster > To: gmx-users@gromacs.org > Message-ID: > <CAB1QHmssKoi4s0nWER+NXMdOs-LSZnexW314SSWre+MQA=eb=g...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hey all, > > I recently ran 20ns simulation of protein ligand complex on cluster i used > following script to run simulation > > grompp -f MD.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o > md_test.tpr > > mpirun -n 8 mdrun -s md_test.tpr -deffnm md_test -np 8 > > *I saved this as MD.sh And then submited to cluster using following script* > > #!/bin/bash > #BSUB -J testgromacs # the job's name/array job > #BSUB -W 120:00 # max. wall clock time in hh:mm > #BSUB -n 8,8 # number of processors Min,Max > #BSUB -o test/output_%J.log # output file > #BSUB -e test/errors_%J.log # error file > #BSUB -M 8192 #Memory limit in MB > > echo "Started at `date`" > echo > > cd test > > echo "Running gromacs test in `pwd`" > > ./MD.sh > > echo "Finished at `date`" > > > It gave result but when checked files .xtc and created RMSD plots in that > x-axis of this plot i see only 8ns ...but in MD.MDP file i specified 20ns.. > > Cluster Output says that "TERM_RUNLIMIT: job killed after reaching LSF run > time limit. > Exited with exit code 140". i gave maximum cluster time 120 hours..still it > is not sufficient .. > > Can any body tell me how do it split script i such that i will get all > 20ns simulation > > > Thanks in advance , > > Sainitin > > > ------------------------------ > > -- > 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! > > End of gmx-users Digest, Vol 108, Issue 154 > ******************************************* > -- > 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
