[gmx-users] Wrong pressure with rigid water

[Mark Abraham]

Hi,

That's not what I suggested you need to think about. Lots of things go into
making a useful physical model, and the fact that so far you think the
pressure is OK is only a tiny part of that. You chose a force field that
was parametrized to work with rigid water. If you use it with something
else, then the burden of proof is on you that your eventual observations
will be a valid model.

Also 750 bar +/- 1000 or with large drift would not be a significant
observation. But only you know these things. Also, you could well have
chosen a volume that is too small because you didn't measure pressure
appropriately during the end of your equilibration phase.

Mark

On Tue, Nov 15, 2016 at 1:19 PM Sudip Das <das.sudip37 at gmail.com> wrote:

> 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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