I' d like to know if I need to check the npt.gro file time by time? I mean is it possible for npt.gro file to reach the equilibrated state and then again become unequilibrated?
Thanks for your suggestions. Sincerely, Shima ________________________________ From: Mark Abraham <mark.j.abra...@gmail.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Monday, January 28, 2013 2:32 PM Subject: Re: [gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory http://www.gromacs.org/Documentation/Terminology/Blowing_Up contains the ideas that will likely help you, e.g. smaller time step, more equilibration-friendly pressure coupling. Mark On Sun, Jan 27, 2013 at 1:59 PM, Shima Arasteh <shima_arasteh2...@yahoo.com>wrote: > > > 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 <jalem...@vt.edu> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > 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 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? 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