Hi Yes, the fluctuations are large but even the average pressure hasn't converged. Its close 2.5 bar. RMSD ~600 bar.
Pooja On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren <dallas.war...@monash.edu>wrote: > See http://www.gromacs.org/Documentation/Terminology/Pressure for further > details > > > > 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 > > +61 3 9909 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Dallas Warren > *Sent:* Wednesday, 8 September 2010 3:21 PM > > *To:* Discussion list for GROMACS users > *Subject:* RE: [gmx-users] Alanine dipeptide simulations > > > > What pressure has it reached? > > > > Probably best graph the pressure versus time plot for the run and show > that. > > > I suspect what you are concerned about is the fact that with pressure > coupling, the pressure can fluctuation from step to step, very widely, 100s > atm is not out of the question. > > > > 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 > > +61 3 9909 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* gmx-users-boun...@gromacs.org [mailto: > gmx-users-boun...@gromacs.org] *On Behalf Of *Sai Pooja > *Sent:* Wednesday, 8 September 2010 3:18 PM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-users] Alanine dipeptide simulations > > > > Hi, > > > I am running an npt simulation on alanine dipeptide in explicit solvent > using charmm forcefield and tip3p. > > The pressure is set to 1bar and the barostat is Parrinello-Rahman. The > simulation has been running for 45 ns and has not achieved the target > average pressure of 1 bar. > > I don;t understand why is this the case. > > My mdp file: > > ; RUN CONTROL PARAMETERS > integrator = md > dt = 0.002 > nsteps = 500000 > > ; OUTPUT CONTROL OPTIONS > nstxout = 0 ; No output, except for > last frame (coordinates) > nstvout = 0 ; No output, except for > last frame (velocities) > nstfout = 0 ; No output, except for > last frame (forces) > nstlog = 5000 ; Write every step to the > log > nstenergy = 5000 ; Write energies at > every step > xtc_grps = Protein SOL > nstxtcout = 5000 ; Do not write a > compressed trajectory > energygrps = Protein SOL ; Write energy information > separately for these groups > > ; NEIGHBORSEARCHING PARAMETERS > nstlist = 5 > ns-type = Grid > pbc = xyz > rlist = 0.9 > > ; OPTIONS FOR ELECTROSTATICS AND VDW > coulombtype = PME > fourierspacing = 0.15 > rcoulomb = 0.9 > vdw-type = Cut-off > rvdw = 1.0 > > ; FFT grid size, when a value is 0 fourierspacing will be used = > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > ; EWALD/PME/PPPM parameters = > pme_order = 4 > ewald_rtol = 1e-05 > epsilon_surface = 0 > optimize_fft = no > ; Temperature coupling > tcoupl = nose-hoover > tc-grps = Protein Non-Protein > tau_t = 0.2 0.2 > ref_t = 300 300 > > ; Pressure coupling > Pcoupl = Parrinello-Rahman > Pcoupltype = Isotropic > tau_p = 1.0 > compressibility = 4.5e-5 > ref_p = 1.0 > > ; OPTIONS FOR BONDS > constraints = all-bonds > > > Pooja > > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > > -- > 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 > -- Quaerendo Invenietis-Seek and you shall discover.
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