[gmx-users] Wrong pressure with rigid water

[Sudip Das]

Dear Mark,

Thanks for your reply.

As rigid water was not giving reasonable pressure, I have tried with
flexible one where pressure is behaving well upto 2 ns of NVT simulation.


Here is the details of my system:

System: Protein in water
# of residues in protein: 188
# of water molecules: 17876
# of NA cation: 3
Box length (after NPT equilibration): 7.13927 nm



Here is the nvt_production.mdp file:


title        = Protein-ligand complex NVT production
;define      = -DFLEXIBLE

; Run parameters
integrator  = md
nsteps      = 200000
dt              = 0.0005
nstcomm          = 1
comm_grps     = system
comm_mode   = linear

; Output control
nstxout     = 200
nstvout     = 200
nstenergy = 200
nstlog       = 200
energygrps  = system

; Bond parameters
continuation    = no
constraints     = none

; Neighborsearching
ns_type     = grid
nstlist     = 5
rlist       = 1.4

rvdw          = 1.4
cutoff-scheme = Verlet
vdwtype       = cut-off

; Electrostatics
rcoulomb        = 1.4
coulombtype     = PME
pme_order       = 4
fourierspacing  = 0.16

; Temperature coupling
tcoupl      = nose-hoover
tc-grps     = system
tau_t       = 1.0
ref_t       = 300

; Pressure coupling
pcoupl      = no

; Periodic boundary conditions
pbc         = xyz

; Dispersion correction
DispCorr    = EnerPres

; Velocity generation
gen_vel     = no



Best regards,
Sudip

On Tue, Nov 15, 2016 at 1:28 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> The solvent models are designed to be rigid, use flexible versions only if
> you know why they will be a good model for you.
>
> Measuring pressure can take nanoseconds, but we don't have enough
> information to know what you've done and its error estimates.
>
> Mark
>
> On Mon, 14 Nov 2016 17:21 Sudip Das <das.sudip37 at gmail.com> wrote:
>
> > Dear All,
> >
> > I am simulating a protein in water with GROMOS96 force field (gromos54a7)
> > and SPC/E water model. After minimization followed by NVT equilibration,
> I
> > performed 2ns of NPT equilibration. From the converged box length I have
> > taken the average value and set the box length (in npt_equilibrium.gro
> > file) to that value and used this for NVT production run.
> >
> > In the production run, temperature, potential and total energies are
> > reasonable, whereas the pressure is behaving weirdly. I have started the
> > NVT production run with 1 bar pressure.
> >
> >
> > NVT production run with flexible water (define = -DFLEXIBLE): P = 1 to 5
> > bar
> >
> > NVT production run with rigid water: P = 750 to 780 bar
> >
> >
> > Did anyone encountered this kind of problem? I would appreciate your kind
> > help in resolving this.
> >
> > Best regards,
> > Sudip
> > --
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