[gmx-users] unstable system
Shima Arasteh
shima_arasteh2001 at yahoo.com
Wed May 8 17:23:40 CEST 2013
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 <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at 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
========================================
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