[gmx-users] (no subject)

[gangotri dey]

Dear all,

I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
have solvated the surface with water in all 3 directions. After the NVT
run, I see that the surface is deformed. I was wondering what else can I
add in my nvt.mdp to not encounter this problem?

I have mainly followed the examples in the forum for graphene/CNT growth.

title           = MnO2  in H2O NVT equilibration
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 50000         ; 2 * 500000 = 100 ps
dt                  = 0.002             ; 2 fs
; Output control
nstxout         = 50            ; save coordinates every 0.10 ps
nstvout         = 50            ; save velocities every 0.10 ps
nstenergy       = 50            ; save energies every 0.10 ps
nstlog          = 50            ; update log file every 0.10 ps
; Bond parameters
continuation            = no            ; first dynamics run
constraint_algorithm    = lincs     ; holonomic constraints
constraints                 = none      ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter                  = 1             ; accuracy of LINCS
lincs_order                 = 4             ; also related to accuracy
; Neighborsearching
cutoff-scheme   = Verlet
ns_type             = grid              ; search neighboring grid cells
nstlist             = 10                ; 20 fs, largely irrelevant with
Verlet
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                 ; modified Berendsen thermostat
tc-grps         = SOL MnO ; three 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 is off
pcoupl          = no            ; no pressure coupling in NVT
; Periodic boundary conditions
pbc             = xyz               ; 3-D PBC
periodic-molecules = yes
; 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        = 188888                ; generate a random seed


*Thank you*

*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254