It is 15 ns of NPT equilibration and I have not got a proper npt output yet to go to the MDrun. Because when I run the -mdrun command, I get fatal error as water molecule can not be settled.
I guess that the system might need more equilibration. These are the settings of my npt.mdp file. The force field which I use is C36. integrator = md ; leap-frog integrator nsteps =250000 ; 2 * 250000 = 500 ps dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 0.2 ps nstvout = 1000 ; save velocities every 0.2 ps nstenergy = 1000 ; save energies every 0.2 ps nstlog = 1000 ; update log file every 0.2 ps continuation = yes ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = h-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.2 ; short-range neighborlist cutoff (in 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 ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = Nose-Hoover ; modified Berendsen thermostat tc-grps = Protein POPC SOL_CL ; two coupling groups - more accurate tau_t = 0.5 0.5 0.5 ; time constant, in ps ref_t = 310 310 310 ; reference temperature, one for each group, in K pcoupl = Parrinello-Rahman ; no pressure coupling in NVT pcoupltype = semiisotropic tau_p = 4 ref_p = 1.01325 1.01325 compressibility = 4.5e-5 4.5e-5 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = no ; account for cut-off vdW scheme ; Velocity generation gen_vel = no ; assign velocities from Maxwell distribution ;gen_temp = 310 ; temperature for Maxwell distribution ;gen_seed = -1 ; generate a random seed nstcomm = 1 comm_mode = Linear comm_grps = Protein_POPC SOL_CL Would you please give me any sugestions? What are the possible problems might be considered? Thanks for your suggestions. Sincerely, Shima ________________________________ From: Justin Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Sunday, January 6, 2013 9:15 AM Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory On 1/6/13 12:33 AM, Shima Arasteh wrote: > Do you mean that I re-run NPT step with the new index file and npt.gro (which > I got from the last NPT equilibration)? That's not clear to me yet. > That's where I'd start. You may have to run the new configuration through the entire equilibration protocol, though. Instability during MD often indicates inadequate equilibration, so whatever your protocol is may not be sufficient as is and may require greater time. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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 -- 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
