[gmx-users] CH3CN solvents breaking the periodic box

[Debashis Sahu]

Dear Gromacs users,
                              I have faced the simulation problem in CH3CN
solvent box. The box is broken in the NPT simulations and the solvent
molecules also scatter. The trajectory and the pdb file is attached. I can
not understand why the simulation is not running well. If any one have an
idea about this problem please help me.
                             ​
 npt.trr
<https://docs.google.com/file/d/0Bz4vUvGCRemJTWdmbnc1SGszX0E/edit?usp=drive_web>
​​
 UN-F-2.pdb
<https://docs.google.com/file/d/0Bz4vUvGCRemJZ3NhSG1iNkFxQkE/edit?usp=drive_web>
​

I have .mdp file of the energy minimization is as follow:

integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0   ; Stop minimization when the maximum force < 1000.0
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 = 1.0 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)


The .mdp file of NPT is as below:

title       = NPT Equilibration
define      = -DPOSRES          ; position restrain
; Run parameters
integrator  = md                ; leap-frog integrator
nsteps      = 200000           ; 2 * 50000 = 100 ps
dt          = 0.002             ; 2 fs
; Output control
nstxout     = 100              ; save coordinates every 2 ps
nstvout     = 100              ; save velocities every 2 ps
nstenergy   = 100              ; save energies every 2 ps
nstlog      = 100              ; update log file every 2 ps
nstcalcenergy        =  1
; Bond parameters
continuation         = no        ; Initial simulation
constraint_algorithm = lincs     ; holonomic constraints
constraints          = all-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 cels
nstlist     = 5                 ; 10 fs
rlist       = 1.0               ; short-range neighborlist cutoff (in nm)
rcoulomb    = 1.0               ; short-range electrostatic cutoff (in nm)
rvdw        = 1.0             ; short-range van der Waals cutoff (in nm)
; 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      = V-rescale             ; Weak coupling for initial
equilibration
tc-grps     = UNK       F     SOL ; two coupling groups - more accurate
tau_t       = 0.1       0.1   0.1   ; time constant, in ps
ref_t       = 300       300   300   ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl              = Parrinello-Rahman     ; Pressure coupling on in NPT,
also weak coupling
pcoupltype          = isotropic     ; uniform scaling of x-y-z box vectors
tau_p               = 2.0           ; time constant, in ps
ref_p               = 1.0           ; reference pressure (in bar)
compressibility     = 4.5e-5        ; isothermal compressibility, bar^-1
refcoord_scaling    = com
; Periodic boundary conditions
pbc     = xyz                   ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres          ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = no               ; Velocity generation is off
gen_temp    = 300               ; temperature for velocity generation
gen_seed    = -1                ; random seed
; COM motion removal
; These options remove COM motion of the system
nstcomm         = 10
comm-mode       = Linear
comm-grps       = System

with warm regards,
*Debashis Sahu*
*Central Salt and Marine Chemical Research Institute*
*Bhavnagar, Gujarat*
*India, 364002.*