On 5/11/13 2:12 AM, Shima Arasteh wrote:
Hi,
The commands are as this:
EM:
minim.mdp :
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 100.0
kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of (minimization) steps to
perform
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long
range forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.2 ; Cut-off for making neighbor list (short range
forces)
rlistlong = 1.4
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; Short-range electrostatic cut-off
rvdw = 1.2 ; Short-range Van der Waals cut-off
vdwtype = switch
rvdw_switch = 1.0
pbc = xyz ; Periodic Boundary Conditions
#grompp -f minim.mdp -c minim_npt_9_mod.pdb -p topol.top -o minim_10.tpr
# mpirun -np 32 mdrun_mpi -deffnm minim_10 -v
Steepest Descents converged to Fmax < 100 in 5865 steps
Potential Energy = -1.5278298e+06
Maximum force = 7.5562675e+01 on atom 71284
Norm of force = 2.8630490e+00
This looks reasonable. If you're using constraints later on, I would suggest
minimizing again with those same constraints before proceeding.
NVT:
nvt.mdp:
title = NVT equilibration for dimer-POPC-water - CHARMM36
define
= -DPOSRES_LIPID -DPOSRES ; P headgroups of POPC and Protein is
position restrained (uses the posres.itp file information)
; Parameters describing the details of the NVT simulation protocol
integrator
= md ; Algorithm ("md" = molecular dynamics [leap-frog
integrator]; "md-vv" = md using velocity verlet; sd = stochastic
dynamics)
dt = 0.001 ; Time-step (ps)
nsteps = 2000000 ; Number of steps to run (0.001 * 20000000 = 2000 ps)
; Parameters controlling output writing
nstxout = 2000 ; Write coordinates to output .trr file every 2 ps
nstvout = 1000 ; Write velocities to output .trr file every 2 ps
nstenergy = 1000 ; Write energies to output .edr file every 2 ps
nstlog = 1000 ; 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 = no ; Whether a fresh start or a continuation from a
previous run (yes/no)
constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
constraints = h-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 = v-rescale ; Modified Berendsen thermostat using
velocity rescaling
tc-grps = Protein_POPC Water_and_ions ; Define groups to be
coupled separately to temperature bath
tau_t = 0.1 0.1 ; Group-wise coupling time constant (ps)
ref_t = 310 310 ; Group-wise reference temperature (K)
; Pressure coupling parameters
pcoupl = no ; Under NVT conditions pressure coupling is not done
; Miscellaneous control parameters
; Dispersion correction
DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for
vdW cut-off
; Initial Velocity Generation
gen_vel = yes ; Generate velocities from Maxwell distribution at
given temperature
gen_temp = 310 ; Specific temperature for Maxwell distribution (K)
gen_seed
= -1 ; Use random seed for velocity generation (integer; -1
means seed is calculated from the process ID number)
; 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
refcoord_scaling = com
REPEAT NVT over minim_10:
#grompp -f nvt.mdp -c minim_10.gro -p topol.top -n index_mod_2.ndx -o nvt_10.tpr
#mpirun -np 42 mdrun_mpi -deffnm nvt_10 -v
NVT passed successfully.
NPT
;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
Why are you turning off dispersion correction after you used it previously?
; 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
#grompp -f npt.mdp -c nvt_10.gro -t nvt_10.cpt -p topol.top -n index_mod_2.ndx
-o npt_10.tpr -pp -maxwarn 1
#mpirun -np 32 mdrun_mpi -deffnm npt_10
NPT passed successfully.
MD
md.mdp :
integrator
= md ; Algorithm ("md" = molecular dynamics [leap-frog
integrator]; "md-vv" = md using velocity verlet; sd = stochastic
dynamics)
dt = 0.001 ; Time-step (1fs)
nsteps = 500000 ; Number of steps to run (0.001 * 500000 = 0.5 ns)
; Parameters controlling output writing
nstxout = 1 ; Write coordinates to output .trr file every 10 ps
nstvout = 5000 ; 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)
Now you're switching the constraint type. You minimized with no constraints,
equilibrated with restraints on h-bonds, and now you're constraining all bonds.
That's probably the source of your problem right there. Some bond between
heavy atoms was never minimized properly, was equilibrated happily because its
bond wasn't restrained, and now you're trying to constrain it. Hence your
simulation immediately fails.
Remain consistent throughout your workflow. If you want to constrain all bonds,
do so during every step.
-Justin
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
#grompp -f md.mdp -c npt_10.gro -t npt_10.cpt -p topol.top -n index_MOD_2.ndx
-o md_0_1.tpr
#mdrun -deffnm md_0_1
The output of mdrun is :
starting mdrun 'Protein'
500000 steps, 500.0 ps.
Step 0, time 0 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001763, max 0.045803 (between atoms 4724 and 4722)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
4722 4719 32.0 0.1603 0.1585 0.1530
4721 4719 31.3 0.1111 0.1118 0.1111
4720 4719 32.8 0.1111 0.1114 0.1111
4718 4716 31.3 0.1111 0.1112 0.1111
4717 4716 33.6 0.1111 0.1117 0.1111
step 0
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.649109, max 18.927546 (between atoms 4720 and 4719)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
231 233 32.1 0.1546 0.1965 0.1538
233 236 48.5 0.1531 0.2415 0.1510
233 235 43.4 0.1119 0.1590 0.1111
233 234 41.6 0.1121 0.1563 0.1111
236 242 61.6 0.1455 0.1731 0.1440
237 239 83.6 0.1376 0.3084 0.1370
242 243 43.3 0.1384 0.1339 0.1368
243 245 78.5 0.1387 0.2446 0.1375
243 244 69.1 0.1092 0.1129 0.1080
239 241 76.4 0.1383 0.3464 0.1375
239 240 72.8 0.0985 0.1805 0.0976
241 247 85.6 0.1380 1.6944 0.1368
241 242 73.4 0.1411 0.3049 0.1400
247 249 87.8 0.1385 1.6202 0.1375
247 248 87.8 0.1091 1.4854 0.1080
4722 4719 65.6 0.1585 2.2749 0.1530
4721 4719 69.0 0.1118 1.8299 0.1111
4720 4719 71.2 0.1114 2.2140 0.1111
4725 4722 172.5 0.1585 0.4254 0.1530
4724 4722 117.0 0.1162 0.4249 0.1111
4723 4722 119.8 0.1150 0.4255 0.1111
4727 4725 81.1 0.1115 0.1977 0.1111
4726 4725 73.1 0.1116 0.2040 0.1111
4730 4728 40.7 0.1112 0.0589 0.1111
4728 4729 33.3 0.1112 0.0617 0.1111
245 249 84.6 0.1381 0.5203 0.1375
245 246 84.0 0.1084 0.3678 0.1080
249 250 82.4 0.1084 0.3844 0.1080
4707 4704 38.1 0.1531 0.1972 0.1530
4710 4707 57.9 0.1533 0.3614 0.1530
4709 4707 43.7 0.1112 0.1560 0.1111
4708 4707 45.0 0.1111 0.1572 0.1111
4713 4710 148.7 0.1575 0.3961 0.1530
4712 4710 81.6 0.1113 0.3191 0.1111
4711 4710 83.5 0.1114 0.3239 0.1111
4715 4713 129.1 0.1157 0.2442 0.1111
4714 4713 140.8 0.1148 0.3025 0.1111
4719 4716 109.1 0.1565 2.5635 0.1530
4718 4716 51.0 0.1112 1.1100 0.1111
4717 4716 53.9 0.1117 1.0950 0.1111
Step 1, time 0.001 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005509, max 0.469113 (between atoms 4728 and 4729)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
233 236 30.2 0.1531 0.1485 0.1510
4728 4729 32.1 0.1112 0.0590 0.1111
4728 4730 39.2 0.1112 0.0561 0.1111
4725 4727 81.0 0.1115 0.1850 0.1111
4725 4726 72.6 0.1116 0.1915 0.1111
4722 4725 169.8 0.1585 0.4552 0.1530
4722 4724 116.2 0.1162 0.4645 0.1111
4722 4723 118.2 0.1150 0.4643 0.1111
4719 4722 66.4 0.1585 2.2611 0.1530
4719 4721 68.2 0.1118 1.7639 0.1111
4719 4720 71.0 0.1114 2.1695 0.1111
4716 4719 111.2 0.1565 2.5385 0.1530
Wrote pdb files with previous and current coordinates
Warning: 1-4 interaction between 4719 and 4726 at distance 2.217 which is
larger than the 1-4 table size 2.200 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size
-------------------------------------------------------
Program mdrun, VERSION 4.5.5
Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/mdlib/pme.c,
line: 538
Fatal error:
2
particles communicated to PME node 4 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
Would you please give me your suggestions?
Sincerely,
Shima
----- Original Message -----
From: Shima Arasteh <shima_arasteh2...@yahoo.com>
To: Justin Lemkul <jalem...@vt.edu>; "gmx-users@gromacs.org"
<gmx-users@gromacs.org>
Cc:
Sent: Wednesday, May 8, 2013 7:53 PM
Subject: Re: [gmx-users] unstable system
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
========================================
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