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.
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