[gmx-users] Wrong pressure with rigid water

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 15 14:33:29 CET 2016 

Hi,

The box size changed over the NPT equilibration. You can't just use the
average size if that includes the non-equilibrated times.

Mark

On Tue, Nov 15, 2016 at 2:30 PM Sudip Das <das.sudip37 at gmail.com> wrote:

> Dear Mark,
>
> Sorry if I misunderstood your point. I am aware that GROMOS force field was
> parametrized to work with rigid water. My aim is also not to use flexible
> water. I have performed the flexible water simulation just for testing
> purpose.
>
> Also the box length is converged (with a 0.0005 nm fluctuation) after the
> NPT equilibration run and I have used this average box length for the NVT
> production run.
>
> In the NPT equilibration, physical quantities like temperature, pressure
> (fluctuating between 1 to 2 bar), energies are behaving well. The same is
> also true for NVT production run, except pressure which is fluctuation
> between 500 to 1000 bar with an average of 750-780 bar.
>
> I am confused about what could be the reason of this high pressure although
> other quantities are behaving well.
>
> Thanks in advanced for your kind suggestions.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 6:03 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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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