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 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 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 Would you please help me? Sincerely, Shima ----- Original Message ----- From: Justin Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Sent: Wednesday, May 8, 2013 2:16 AM Subject: Re: [gmx-users] unstable system On 5/7/13 2:42 PM, Shima Arasteh wrote: > Hi, > > I have run a new npt after energy minimization on my system composed of > water/protein/lipid/ions. > After a few nanoseconds for NPT, I ran MD, and got fatal error : > > > X particles communicated to PME node Y are more than a cell length out >of > the domain decomposition cell of their charge group > > > > What is written in md.log file shows an improper pressure, > Step Time Lambda > 0 0.00000 0.00000 > > Energies (kJ/mol) > U-B Proper Dih. Improper Dih. CMAP Dih. LJ-14 > 8.26284e+04 5.54129e+04 7.43891e+02 -1.96405e+02 8.37087e+03 > Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) Coul. recip. > -1.05973e+05 8.51736e+04 -5.79669e+03 -1.11865e+06 -2.67464e+05 > Position Rest. Potential Kinetic En. Total Energy Temperature > 2.09408e+03 -1.26366e+06 3.33724e+05 -9.29932e+05 4.44648e+02 > Pres. DC (bar) Pressure (bar) Constr. rmsd > -1.09245e+02 -2.40668e+04 6.65938e-04 > > > I' d like to know if it means that more that the system is required of more > npt > equilibration? > > Thanks for your suggestion. Please help me. > There is no reason why NPT should run stably but MD would then fail. The high initial temperature suggests that atoms are overlapping somehow or that the previous state has not been preserved properly. Please provide exact details of what you are doing, including the following: 1. Exact commands given in the preparation protocol (EM and equilibration) 2. The .mdp files being used for all steps, most importantly NPT and MD 3. Your grompp and mdrun invocations for the failing MD run -Justin > ----- Original Message ----- > From: Justin Lemkul <[email protected]> > To: Shima Arasteh <[email protected]>; Discussion list for GROMACS > users <[email protected]> > Cc: > Sent: Friday, April 19, 2013 11:29 PM > Subject: Re: [gmx-users] unstable system > > > > On 4/19/13 2:57 PM, Shima Arasteh wrote: > > Thanks so much for your replies. I appreciate you. > > Do you think that more NPT equilibration might solve the problem? or wont >work? > > > > > > I have no idea at what point you are in your procedure that is crashing. I'm > not going to make some blind assessment of "do more NPT" or some random thing. > If you just completed the EM as you posted, proceed with whatever > equilibration > protocol you believe to be sufficient. There is no one single answer here. > If > you're jumping straight into MD after the EM you showed, you need to start > your > equilibration over again completely. > > -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 > > ======================================== -- ======================================== 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
