[gmx-users] Alanine dipeptide simulations

[Sai Pooja]

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>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
>
> +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] *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
>
> +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] *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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