Hi Justin Thank you very much for your comments. I actually found that after posting the question. sorry I have a new question i did NPT equilibration of DCE molecules and the average pressure turns out to be 3.4726 (bar) where as i want the pressure it to be 1 bar. what further i need to do?.below is what i got from the g_energy command.
Energy Average RMSD Fluct. Drift Tot-Drift ------------------------------------------------------------------------------- Pressure (bar) 3.47263 767.297 765.878 0.8078 161.561 below is my mdp file any help is highly appreciated title = DCE NVT equilibration cpp = usr/bin/cpp integrator = md nsteps = 200000 dt = 0.001 nstxout = 1000 nstvout = 1000 nstenergy = 1000 nstlog = 1000 constraint_algorithm = shake constraints = none unconstrained_start = yes shake_tol = 0.0001 morse = no ns_type = grid nstlist = 5 rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = Cut-off rvdw = 1.0 pme_order = 4 fourierspacing = 0.16 pbc = xyz tcoupl = V-rescale tc-grps = system tau_t = 0.1 ref_t = 300 pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau_p = 2.0 2.0 ref_p = 1.0 1.0 compressibility = 0.0 4.5e-5 DispCorr = Enerpres gen_vel = yes gen_temp = 300 gen_seed = 173529 Regards Vinoth On Tue, Oct 26, 2010 at 4:34 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi Dallas / all >> >> I looked up at the pressure coupling section and i found how to keep the >> box size same for two axis and change only one axis (i used semiisotropic >> pressure coupling type) but when i did that the average pressure i get after >> the run is negative where as i want it be close to 1 bar?. i dont know what >> might have gone wrong. >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> >> ------------------------------------------------------------------------------- >> Pressure (bar) -661.673 675.593 674.292 -0.725677 >> -145.136 >> >> similary when i give g_energy -f npt.edr -o density.xvg the density option >> is not there to select it interactively. hence i am not able to plot the >> density graph.why? >> >> > All of the above suggests you've gotten your files confused and you're > analyzing an .edr file from an NVT run, not NPT. If indeed you did NPT, the > density term would appear below, along with "Volume." The only time when > these terms are not written is if the volume of the unit cell is static > (i.e., NVT). > > > > 1 Bond 2 Angle 3 Ryckaert-Bell. 4 LJ-14 >> 5 Coulomb-14 6 LJ-(SR) 7 Disper.-corr. 8 Coulomb-(SR) >> 9 Coul.-recip. 10 Potential 11 Kinetic-En. 12 Total-Energy >> 13 Conserved-En. 14 Temperature 15 Pressure-(bar) 16 Vir-XX >> 17 Vir-XY 18 Vir-XZ 19 Vir-YX 20 Vir-YY >> 21 Vir-YZ 22 Vir-ZX 23 Vir-ZY 24 Vir-ZZ >> 25 Pres-XX-(bar) 26 Pres-XY-(bar) 27 Pres-XZ-(bar) 28 >> Pres-YX-(bar) >> 29 Pres-YY-(bar) 30 Pres-YZ-(bar) 31 Pres-ZX-(bar) 32 >> Pres-ZY-(bar) >> 33 Pres-ZZ-(bar) 34 #Surf*SurfTen 35 Mu-X 36 Mu-Y >> 37 Mu-Z 38 T-System 39 Lamb-System >> >> and i have given my mdp file below. any help is highly appreciated. >> >> title = DCE NPT equilibration >> integrator = md nsteps = 200000 >> dt = 0.001 nstxout = 1000 nstvout = 1000 >> nstenergy = 1000 nstlog = 1000 >> constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 >> lincs_order = 4 ns_type = grid nstlist = 5 rlist >> = 1.0 rcoulomb = 1.0 rvdw = 1.0 coulombtype = >> PME pme_order = 4 fourierspacing = 0.16 tcoupl = >> V-rescale tc-grps = system tau_t = 0.1 ref_t = 300 >> pcoupl = Parrinello-Rahman pcoupltype = semiisotropic >> tau_p = 2.0 2.0 ref_p = 1.0 1.0 compressibility = >> 0.0 4.5e-5 >> > > For what its worth, if this is your initial equilibration, using > Parrinello-Rahman coupling may not be your best choice. If your system is > far from equilibrated, the P-R method (in my experience) can allow for wide > oscillations, and ultimately system instability. Nothing wrong with > Berendsen for your initial equilibration. > > But again, if pressure coupling was actually used, you'd have Volume and > Density terms in the .edr file, along with a more sensible value of > pressure. > > -Justin > > pbc = xyz DispCorr = EnerPres gen_vel = no >> Regards >> Vinoth >> >> >> On Tue, Oct 26, 2010 at 5:33 AM, Dallas Warren >> <dallas.war...@monash.edu<mailto: >> dallas.war...@monash.edu>> wrote: >> >> >I performed md simulation of 108 dichloroethane molecules in >> isothermal-isobaric ensemble with the box size >> >> >3.002*2.17*2.17. after the simulation my box size has changed >> considerably from the initial size to 2.87882 2.08095 >> >> >2.08095.why this happens? >> >> >> Density was obviously too lower under the conditions of the >> simulation. Look at the change of pressure, volume and density for >> the box during that simulation. >> >> >> >my second question is can i have a control over the box dimensions >> changes during md (i.e when the box dimensions >> >> >changes during md i want to change it only on one axis(say x >> axis) and want to keep the length of the other two axis (say >> >> >y and z) same as that of my initial box size? any help is highly >> apprecited. >> >> >> Look at the pressure coupling settings, look at anisotropic pressure >> coupling. >> >> >> Catch ya, >> >> Dr. Dallas Warren >> >> Medicinal Chemistry and Drug Action >> >> Monash Institute of Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@monash.edu <mailto:dallas.war...@monash.edu> >> >> >> +61 3 9903 9304 >> --------------------------------- >> When the only tool you own is a hammer, every problem begins to >> resemble a nail. >> >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > 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 >
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