On 6/1/15 4:40 AM, Ming Tang wrote:
Dear gromacs experts, I tried to equilibrate a triple helix using NPT, and the .mdp file is like this: DEFINE = -DPOSRES integrator = md dt = 0.0009 nsteps = 1000000 nstxout = 0 nstvout = 0 nstlog = 10000 nstxtcout = 10000 xtc-precision = 10 cutoff-scheme = verlet coulombtype = reaction-field-zero coulomb-modifier = potential-shift-verlet rcoulomb-switch = 0.8 rcoulomb = 1.4 epsilon_r = 15 vdw-modifier = force-switch rvdw-switch = 0.8 rvdw = 1.4 tcoupl = v-rescale tc-grps = Protein non-protein tau-t = 1.0 1.0 ref-t = 310 310 Pcoupl = parrinello-Rahman Pcoupltype = isotropic tau-p = 5 compressibility = 3e-4 ref-p = 1.0 refcoord_scaling = all pbc = xyz freezegrps = C freezedim = Y Y Y C is a group containing atoms of both the first and the last residues in all the three chains. But after 18ns' simulation, I found the one end of the triple helix moved. Could you help to tell me whether this is normal or there is something wrong with my simulation? Then, I tried to use berendsen for both tcoupl and pcoupl. It turned out that both ends were fixed. I need to keep the original geometry shape of the triple helix, but berendsen algorithm is believed to be inaccurate.
Freezing and pressure coupling are incompatible; see notes in the manual. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
