[gmx-users] unstable system
Shima Arasteh
shima_arasteh2001 at yahoo.com
Wed May 8 08:35:32 CEST 2013
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 <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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 <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS
> users <gmx-users at gromacs.org>
> 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
========================================
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