Yes, all steps were completed successfully. About your tips, OK sir. I' m going to go through the minimization and NVT and NPT again. Lets get my result, then will post the exact commands.
Thanks for your suggestions. Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Wednesday, May 8, 2013 5:07 PM Subject: Re: [gmx-users] unstable system On 5/8/13 2:35 AM, Shima Arasteh wrote: > OK. > > 1. Exact commands given in the preparation protocol (EM and equilibration) > > EM: > # grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr > #mdrun -deffnm minim > > NVT: > #grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr > #mdrun -deffnm nvt -v > > NPT: > # grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr > # mdrun_mpi -deffnm npt > > > *** Next removed some disturbing water molecules, so edited topol file and > made a new index file index_mod_2.ndx: > Ran a new EM: > # grompp -f npt.mdp -c npt_mod.gro -p topol.top -o npt_minim.tpr > # mdrun -deffnm npt_minim > > > Ran a new NPT: > # grompp -f npt.mdp -c npt_minim.gro -p topol.top -n index_mod_2.ndx -o > npt.tpr > # mdrun_mpi -deffnm npt > > I repeated the NPT the same as above in 3 steps: > a) restraints on lipid phosphorous and protein for 1 ns > > b) restraints on protein for 1ns > > c) restraint on protein with less force for 2 ns > All 3 of these steps complete successfully? > > MD: > # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index_mod_2.ndx -o > md_0_1.tpr > # mdrun -deffnm npt > There are a few discrepancies in the commands you have shown here, in particular naming differences between input and output file names. I ask for exact commands (not what you think you remember) for a very important reason - the diagnostic information you have provided (from the .log file) seems to indicate that the previous equilibrated state was not passed along to the MD step, so I suspect you've left out a checkpoint file somewhere or you have regenerated velocities by accident. As a tip, write all of your commands in a shell script and execute the script. Then, if something goes wrong and someone asks for exact commands, just copy and paste. I still can't tell if this is actually what you did. > > 3 particles communicated to PME node 2 are more than 2/3 times the cut - > off out of the domain decomposition cell of their charge group in > dimension y. > This usually means that your system is not well equilibrated. > > > 2. The .mdp files being used for all steps, most importantly NPT and MD > > npt.mdp: > > ;NPT equlibration Dimer-POPC-Water - CHARMM36 > define = -DPOSRES > integrator = md ; leap-frog integrator > nsteps =1000000 ; 1 * 1000000 = 1000 ps > dt = 0.001 ; 1 fs > ; Output control > nstxout = 2000 ; save coordinates every 0.4 ps > nstvout = 2000 ; 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 = 1.0 > ; 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 Water_and_ions ; two coupling groups - > more accurate > tau_t = 0.5 0.5 ; time constant, in ps > ref_t = 310 310 ; reference temperature, one for each group, > in K > pcoupl = Berendsen ; 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 Water_and_ions > refcoord_scaling = com > > > md.mdp: > > title = Production run forGLC-Water-POPC system > define = -DPOSRES > ; Parameters describing the details of the NVT simulation protocol > integrator = md > dt = 0.001 > nsteps = 2500000 ; Number of steps to run (0.002 * 2500000 = 5 ns) > > ; Parameters controlling output writing > nstxout = 1000 ; Write coordinates to output .trr file every 10 > ps > nstvout = 2000 ; Write velocities to output .trr file every 10 ps > nstenergy = 1000 ; Write energies to output .edr file every 2 ps > nstlog = 5000 ; Write output to .log file every 2 ps > ; 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 Coulombic interactions cut-off > distance (nm) > rvdw = 1.2 ; Short-range van der Waals cutoff distance (nm) > pbc = xyz ; Direction in which to use Perodic Boundary > Conditions (xyz, xy, no) > vdwtype = switch > rvdw_switch = 1.0 > ; Parameters for treating bonded interactions > continuation = yes ; 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_POPC Water_and_ions ; Define groups to be > coupled separately to temperature bath > tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps) > ref_t = 310 310 ; Group-wise reference temperature (K) > > ; Pressure coupling parameters > pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT > conditions > pcoupltype = semiisotropic ; Isotropic scaling in the x-y > direction, independent of the z direction > tau_p = 2.0 ; Coupling time constant (ps) > ref_p = 1.01325 1.01325 ; Reference pressure for coupling, x-y, > z directions (bar) > compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility > (bar^-1) > > ; Miscellaneous control parameters > ; Dispersion correction > DispCorr = EnerPres ; Dispersion corrections for Energy and > Pressure for vdW cut-off > ; Initial Velocity Generation > gen_vel = no ; Velocity is read from the previous run > ; Centre of mass (COM) motion removal relative to the specified groups > nstcomm = 1 ; COM removal frequency (steps) > comm_mode = Linear ; Remove COM translation (linear / angular / no) > comm_grps =Protein_POPC Water_and_ions ; COM removal relative to the > specified groups > > I see no explanation as to why the run fails, aside from what I have said above. -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
