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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