Hello All, I am doing all-atom simulation with charmm 36 ff (obtained from reverse CG using the script provided by Tsjerk) The system consists of popc, 21 AA protein, water and ions.
After reverse CG I did short EM and 5 ns NVT simulation. However, when I do NPT simulation, the area per lipid drops from 67 ang2 to 57 within 1 ns ( x and y dimensions decrese and z increases). I am using semiisotropic pressure coupling. I have a question regarding that. I noticed in example .mdps and the tutorial by Justin Lemkul http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/npt.mdp http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/Files/md.mdp tau_p is specified, the ref_p and compresibility is same, does not that mean essentially I am doing isotropic coupling? I am confused what values should be used. Please suggest. Thanks, sxn *md.mdp:* ; RUN CONTROL PARAMETERS dt = 0.002 ;nsTEPS = 12500000 ;25ns nsTEPS = 25000000 ;50ns integrator = md ld-seed = -1 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 10 ; OUTPUT CONTROL OPTIONS ; Output frequency for coords (x), velocities (v) and forces (f) nstxout = 50000 nstvout = 50000 energygrps = Protein Non-Protein ; Output frequency for energies to log file and energy file nstlog = 100 nstcalcenergy = -1 nstenergy = 100 nstxtcout = 500 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 1 rlist ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz, no, xy pbc = xyz periodic_molecules = no ; nblist cut-off rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.2 fourierspacing = 0.16 pme_order = 4 optimize-fft = yes ; Method for doing Van der Waals vdw-type = switch ; cut-off lengths rvdw-switch = 1.0 rvdw = 1.2 ; OPTIONS FOR BONDS constraints = none ; Type of constraint algorithm constraint-algorithm = Lincs lincs-order = 6 ; temperature controls tcoupl = v-rescale tc-grps = Protein Non-Protein tau-t = 1.0 1.0 ref-t = 303 303 ; Pressure Controls pcoupl = Parrinello-Rahman pcoupltype = semiisotropic tau-p = 1.0 ref-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.