Am I supposed to skip this step?
Thanks for your reply. Sincerely, Shima _______________________________ From: Dr. Vitaly Chaban <vvcha...@gmail.com> To: gmx-us...@gromuracs.org 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 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 -- 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