[gmx-users] Alanine dipeptide simulations
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 8 12:55:53 CEST 2010
Did you do any form of equilibration prior to the production run? If so, what?
In my experience, an incompletely (or improperly) equilibrated system that is
passed to the P-R barostat can lead to undesired pressures. As long as there
are no systematic influences on your pressure (i.e., trending up or down), then
you've probably got a stable simulation, especially given the fluctuations.
-Justin
Sai Pooja wrote:
> So, what should I aim for when running an NPT simulation?
>
> Pooja
>
> On Wed, Sep 8, 2010 at 1:42 AM, Dallas Warren <Dallas.Warren at monash.edu
> <mailto:Dallas.Warren at monash.edu>> wrote:
>
> Is that really that surprising?
>
>
>
> You have variations of the order of 100s of bar and are looking for
> an average that is 1.0
>
>
>
> What you are observing is nothing out of the ordinary, from my
> experience and what others have discussed here on the emailing list.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
> +61 3 9909 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
>
>
>
> *From:* gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [mailto:gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Sai Pooja
> *Sent:* Wednesday, 8 September 2010 3:38 PM
>
> *To:* Discussion list for GROMACS users
> *Subject:* Re: [gmx-users] Alanine dipeptide simulations
>
>
>
> Hi
>
> Yes, the fluctuations are large but even the average pressure hasn't
> converged. Its close 2.5 bar. RMSD ~600 bar.
>
> Pooja
>
> On Wed, Sep 8, 2010 at 1:27 AM, Dallas Warren
> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> wrote:
>
> See http://www.gromacs.org/Documentation/Terminology/Pressure for
> further details
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
> +61 3 9909 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
>
>
>
> *From:* gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [mailto:gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Dallas Warren
> *Sent:* Wednesday, 8 September 2010 3:21 PM
>
>
> *To:* Discussion list for GROMACS users
>
> *Subject:* RE: [gmx-users] Alanine dipeptide simulations
>
>
>
> What pressure has it reached?
>
>
>
> Probably best graph the pressure versus time plot for the run and
> show that.
>
>
> I suspect what you are concerned about is the fact that with
> pressure coupling, the pressure can fluctuation from step to step,
> very widely, 100s atm is not out of the question.
>
>
>
> Catch ya,
>
> Dr. Dallas Warren
>
> Medicinal Chemistry and Drug Action
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
> +61 3 9909 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.
>
>
>
> *From:* gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>
> [mailto:gmx-users-bounces at gromacs.org
> <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Sai Pooja
> *Sent:* Wednesday, 8 September 2010 3:18 PM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Alanine dipeptide simulations
>
>
>
> Hi,
>
>
>
> I am running an npt simulation on alanine dipeptide in explicit
> solvent using charmm forcefield and tip3p.
>
> The pressure is set to 1bar and the barostat is Parrinello-Rahman.
> The simulation has been running for 45 ns and has not achieved the
> target average pressure of 1 bar.
>
> I don;t understand why is this the case.
>
> My mdp file:
>
> ; RUN CONTROL PARAMETERS
> integrator = md
> dt = 0.002
> nsteps = 500000
>
> ; OUTPUT CONTROL OPTIONS
> nstxout = 0 ; No output, except
> for last frame (coordinates)
> nstvout = 0 ; No output, except
> for last frame (velocities)
> nstfout = 0 ; No output, except
> for last frame (forces)
> nstlog = 5000 ; Write every step to
> the log
> nstenergy = 5000 ; Write energies
> at every step
> xtc_grps = Protein SOL
> nstxtcout = 5000 ; Do not write a
> compressed trajectory
> energygrps = Protein SOL ; Write energy information
> separately for these groups
>
> ; NEIGHBORSEARCHING PARAMETERS
> nstlist = 5
> ns-type = Grid
> pbc = xyz
> rlist = 0.9
>
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> coulombtype = PME
> fourierspacing = 0.15
> rcoulomb = 0.9
> vdw-type = Cut-off
> rvdw = 1.0
>
> ; FFT grid size, when a value is 0 fourierspacing will be used =
> fourier_nx = 0
> fourier_ny = 0
> fourier_nz = 0
> ; EWALD/PME/PPPM parameters =
> pme_order = 4
> ewald_rtol = 1e-05
> epsilon_surface = 0
> optimize_fft = no
> ; Temperature coupling
> tcoupl = nose-hoover
> tc-grps = Protein Non-Protein
> tau_t = 0.2 0.2
> ref_t = 300 300
>
> ; Pressure coupling
> Pcoupl = Parrinello-Rahman
> Pcoupltype = Isotropic
> tau_p = 1.0
> compressibility = 4.5e-5
> ref_p = 1.0
>
> ; OPTIONS FOR BONDS
> constraints = all-bonds
>
>
> Pooja
>
>
>
>
> --
> Quaerendo Invenietis-Seek and you shall discover.
>
>
> --
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> --
> Quaerendo Invenietis-Seek and you shall discover.
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> Quaerendo Invenietis-Seek and you shall discover.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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