[gmx-users] nvt problem

[Lovika Moudgil]

Hi Everyone ,

I am having a problem in NVT of system . In my system I have Gold and
aminoacid . For Gold I am using GolP forcefield and for aminoacid using
OPLSAA forcefield . I have done energy minimization of my system but when I
am doing NVT I am getting error of water is not getting settled . I am
confused How it got minimize if water is not settled in system .I have
tried changing parameters of NVT.mdp file but noting worked . Can any body
help me what can be the root cause for this . I will be thankful for
guidance .

My NVT.mdp
; 7.3.2 Preprocessing
define                  = -DPOSRES      ; defines to pass to the
preprocessor

; 7.3.3 Run Control
integrator              = md                    ; md integrator
tinit                   = 0                     ; [ps] starting time for run
dt                      = 0.001                 ; [ps] time step for
integration
nsteps                  = 25000                 ; maximum number of steps
to integrate, 0.001 * 25,000 = 25 ps
nstcomm                 = 1                     ; [steps] frequency of mass
motion removal
comm_grps               = Protein Non-Protein   ; group(s) for center of
mass motion removal

; 7.3.8 Output Control
nstxout                 = 25000         ; [steps] freq to write coordinates
to trajectory
nstvout                 = 25000         ; [steps] freq to write velocities
to trajectory
nstfout                 = 25000         ; [steps] freq to write forces to
trajectory
nstlog                  = 50           ; [steps] freq to write energies to
log file
nstenergy               = 100           ; [steps] freq to write energies to
energy file
nstxtcout               = 100           ; [steps] freq to write coordinates
to xtc trajectory
xtc_precision           = 1000          ; [real] precision to write xtc
trajectory
xtc_grps                = System        ; group(s) to write to xtc
trajectory
energygrps              = System        ; group(s) to write to energy file

; 7.3.9 Neighbor Searching
nstlist                 = 1             ; [steps] freq to update neighbor
list
ns_type                 = grid          ; method of updating neighbor list
pbc                     = xyz           ; periodic boundary conditions in
all directions
rlist                   = 1.4           ; [nm] cut-off distance for the
short-range neighbor list

; 7.3.10 Electrostatics
coulombtype             = PME           ; Particle-Mesh Ewald electrostatics
rcoulomb                = 1.4           ; [nm] distance for Coulomb cut-off

; 7.3.11 VdW
vdwtype                 = cut-off       ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw                    = 1.4           ; [nm] distance for LJ cut-off
DispCorr                = EnerPres      ; apply long range dispersion
corrections

; 7.3.13 Ewald
fourierspacing          = 0.10          ; [nm] grid spacing for FFT grid
when using PME
pme_order               = 4             ; interpolation order for PME, 4 =
cubic
ewald_rtol              = 1e-5          ; relative strength of
Ewald-shifted potential at rcoulomb

; 7.3.14 Temperature Coupling
tcoupl                  = nose-hoover                     ; temperature
coupling with Berendsen-thermostat
tc_grps                 = Protein    Non-Protein        ; groups to couple
seperately to temperature bath
tau_t                   = 0.1        0.1                ; [ps] time
constant for coupling
ref_t                   = 310        310                ; [K] reference
temperature for coupling

; 7.3.17 Velocity Generation
gen_vel                 = no           ; generate velocities according to
Maxwell distribution of temperature
gen_temp                = 310           ; [K] temperature for Maxwell
distribution
gen_seed                = -1            ; [integer] used to initialize
random generator for random velocities

; 7.3.18 Bonds
constraints             = all-bonds     ; convert all bonds to constraints
constraint_algorithm    = LINCS         ; LINear Constraint Solver
lincs_order             = 4             ; highest order in the expansion of
the contraint coupling matrix
lincs_iter              = 1             ; number of iterations to correct
for rotational lengthening
lincs_warnangle         = 80            ; [degrees] maximum angle that a
bond can rotate before LINCS will complain
; To keep au surface in place, freeze Au atoms.
; The AU group has been defined via make_ndx
; to contains all the AU atoms ('a AU').
freezegrps               = AU  AUI
freezedim                = Y Y Y Y Y Y
comm_mode                 = none



Regards
Lovika