[gmx-users] Wrong pressure with rigid water
Sudip Das
das.sudip37 at gmail.com
Wed Nov 16 08:42:48 CET 2016
Hi Mark,
The problem is resolved.
Previously, I was using rlist = rvdw = rcoulomb = 1.2, which leads to high
pressure from NVT run. NPT equilibrated avg box length (7.13927 nm) was
used for NVT run.
But I got correct pressure by using rlist = rvdw = rcoulomb = 1.4 (suitable
for GROMOS force field). NPT equilibrated avg box length (7.2115 nm) is
used for NVT run.
Thanks for your kind replies.
Best regards,
Sudip
On Tue, Nov 15, 2016 at 7:05 PM, Sudip Das <das.sudip37 at gmail.com> wrote:
> Dear Mark,
>
> I have forgot to mention one point. All the data that are provided in the
> previous mail, are for simulation with rigid water molecules.
>
> Best regards,
> Sudip
>
> On Tue, Nov 15, 2016 at 7:00 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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>>
>>
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