[gmx-users] Problem while running equilibration

[Nirali Desai]

Dear all,

My system consists of a three chains of protein: PROA, PROB and PROCLIG
(with ligand).
Minimization is running properly without any error.
Parameters used are:
title = Minimization ; Title of run
define          = -DPOSRES

; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000   ; Stop minimization when the maximum force < 10.0 kJ/mol
emstep      = 0.01      ; Energy step size
nsteps = 50000   ; Maximum number of (minimization) steps to perform
energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
SOL
freezegrps      = PROCLIG
freezedim       = Y Y Y

But, while running equilibration it is giving error of the blowing up of
the system like water molecule not settled, clashes etc.
I ran the equilibration without adding water and also without using freeze
groups. It is running perfectly. I turned off constraints and pressure
coupling while using freezegroups.
 Parameters used:

title       = Protein-ligand complex NVT equilibration
define      = -DPOSRES  ; position restrain the protein and ligand
; Run parameters
integrator  = md        ; leap-frog integrator
nsteps      = 50000     ; 2 * 50000 = 100 ps
dt          = 0.002     ; 2 fs
; Output control
nstxout     = 100       ; save coordinates every 0.2 ps
nstvout     = 100       ; save velocities every 0.2 ps
nstenergy   = 100       ; save energies every 0.2 ps
nstlog      = 100       ; update log file every 0.2 ps
energygrps = PROA PROB PROCLIG SOL ; Which energy group(s) to write to disk
energygrp_excl  = PROA PROA PROB PROB PROCLIG PROCLIG SOL SOL PROA SOL PROB
SOL
freezegrps      = PROCLIG
freezedim       = Y Y Y
; Bond parameters
continuation    = no            ; first dynamics run
constraints     = none     ; all bonds (even heavy atom-H bonds) constrained
; Neighborsearching
ns_type     = grid      ; search neighboring grid cells
cutoff-scheme  = group
nstlist     = 20         ; 10 fs
rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
rvdw        = 0.9       ; 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
tcoupl      = V-rescale                     ; modified Berendsen thermostat
tc-grps     = Protein non-protein   ; two coupling groups - more accurate
tau_t       = 0.1   0.1                     ; time constant, in ps
ref_t       = 300   300                     ; reference temperature, one
for each group, in K
; Pressure coupling
pcoupl      = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc         = xyz       ; 3-D PBC
; Dispersion correction
DispCorr    = EnerPres  ; account for cut-off vdW scheme
; Velocity generation
gen_vel     = yes       ; assign velocities from Maxwell distribution
gen_temp    = 300       ; temperature for Maxwell distribution
gen_seed    = -1        ; generate a random seed

Please guide me on this.
If you have any suggestions I will really appreciate.

Thanks and regards,
Nirali