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On Mon, Jan 28, 2013 at 12:51 PM, Shima Arasteh <[email protected]> wrote: > > > Am I supposed to skip this step? > > > Thanks for your reply. > > Sincerely, > Shima > _______________________________ > From: Dr. Vitaly Chaban <[email protected]> > To: [email protected] > Sent: Monday, January 28, 2013 3:17 PM > Subject: [gmx-users] Re: Protein in vacum > >> >> Dear users, >> >> I have done simulation with my protein in water earlier successfully using >> CHARMM36 FF. Now, I am trying to simulate protein in vacum similar to the >> last simulation of protein-water. When I go to the NPT equilibration, I get >> a fatal error. >> The commands I ran: >> >> The npt.mdp file settings are: >> ; Parameters describing neighbors searching and details about interaction >> calculations >> ns_type = grid ; Neighbor list search method (simple, grid) >> nstlist = 5 ; Neighbor list update frequency (after every >> given number of steps) >> rlist = 1.2 ; Neighbor list search cut-off distance (nm) >> rlistlong = 1.4 >> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm) >> rvdw = 1.2 ; short-range van der Waals cutoff (in nm) >> vdwtype = switch >> rvdw_switch = 0.8 >> ; Parameters for treating bonded interactions >> continuation = no ; Whether a fresh start or a continuation from a >> previous run (yes/no) >> constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) >> constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / >> hbonds / none / all-angles / h-angles) >> lincs_iter = 1 ; Number of iterations to correct for rotational >> lengthening in LINCS (related to accuracy) >> lincs_order = 4 ; Highest order in the expansion of the constraint >> coupling matrix (related to accuracy) >> >> ; Parameters for treating electrostatic interactions >> coulombtype = PME ; Long range electrostatic interactions >> treatment (cut-off, Ewald, PME) >> pme_order = 4 ; Interpolation order for PME (cubic interpolation >> is represented by 4) >> fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using >> PME (nm) >> >> ; Temperature coupling parameters >> tcoupl = Nose-Hoover ; Modified Berendsen thermostat using >> velocity rescaling >> tc-grps = Protein ; Define groups to be coupled separately to >> temperature bath >> tau_t = 0.5 ; Group-wise coupling time constant (ps) >> ref_t = 310 ; Group-wise reference temperature (K) >> >> ; Pressure coupling parameters >> pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT >> conditions >> pcoupltype = isotropic ; Isotropic scaling in the x-y >> direction, independent of the z direction >> tau_p = 5.0 ; Coupling time constant (ps) >> ref_p = 1.0 ; Reference pressure for coupling, x-y, z >> directions (bar) >> compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility >> (bar^-1) >> refcoord_scaling = com > > > > Vacuum is incompatible with pressure coupling. > > > Dr. Vitaly V. Chaban > MEMPHYS - Center for Biomembrane Physics > Department of Physics, Chemistry and Pharmacy > University of Southern Denmark > Campusvej 55, 5230 Odense M, Denmark > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
