[gmx-users] parameters obtained after NPT

[soumadwip ghosh]

Dear users,

                 Firstly, I would like to thank Justin for helping me out
in preparing  an initial system containing a single walled CNT and a ss-DNA
for MD simulations. Previously I was using position restraint as well as
freeze group for keeping my CNT fixed during equilibration steps and the
system was blowing up and it was not minimized well. Now, I am  stuck with
a new problem is that after the NPT run for about 5 ns, I am getting some
weird pressure, density and volume from g_energy. The pressure is negative
and the volume is nowhere close to the initial cell volume. Although the
temperature is alright but the density is in hundreds while for TIP3P water
models it should be around 1020 Kg M(-3). I want to see the volume (cell)
reaching the desired values along with proper build-up of density and
that's why I started NPT first instead of NVT. Is it happening because the
npt.mdp file is wrong somewhere? Please help me out with this. I am using
GROMACS 4.5.6 in conjugation with CHARMM 27 force field. The .mdp file is
given below.


title           = ssdna          npt equilibration
define          = -DPOSRES      ; position restrain the dna
; Run parameters
integrator      = md            ; leap-frog integrator
nsteps          = 4000000               ; 2 * 1000000 = 2000 ps
dt              = 0.002         ; 2 fs
; Output control
nstxout         = 500           ; save coordinates every 0.2 ps
nstvout         = 500           ; save velocities every 0.2 ps
nstenergy       = 500           ; save energies every 0.2 ps
nstlog          = 1000          ; update log file every 0.2 ps
; Bond parameters
continuation    = yes           ; Restarting after NVT
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 cells
nstlist         = 5             ; 10 fs
rlist           = 1             ; short-range neighborlist cutoff (in nm)
rcoulomb        = 1             ; short-range electrostatic cutoff (in nm)
rvdw            = 1             ; 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         = SYSTEM        ; three coupling groups - more accurate
tau_t           = 0.1           ; time constant, in ps
ref_t           = 300           ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl          = berendsen     ; Pressure coupling on in NPT
pcoupltype      = isotropic     ; uniform scaling of box vectors
tau_p           = 2.0           ; time constant, in ps
ref_p           = 1.0           ; reference pressure, in bar
compressibility = 4.5e-5        ; isothermal compressibility of water,
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

Thank you for your time in advance.

Regards,
Soumadwip Ghosh
Research Fellow,
IITB, mumbai
India