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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