[gmx-users] Pressure Fluctuations

[Kavyashree M]

Thank you Sir

   I am using OPLSAA with tip4p water model, I agree to the fact that
it will oscillate but the oscillation is this case was from appr. -1000bar
to 1000bar. And as it is stated in the FAQ regarding the variation of
fluctuations with number of waters, this system has 6882 waters along
with a protein of 123 aa, so is not this fluctuations high?
   Pressure coupling used -parinello-rahman
  tau_p = 2.0
  tau_t  = 1.0
  compressibility 4.5e-5
  Pcouple_type = isotropic

Any suggestions?

Thanking you
With Regards
M. Kavyashree

On Wed, Mar 16, 2011 at 12:10 PM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> On 16/03/11, *Kavyashree M * <hmkvsri at gmail.com> wrote:
>
> Dear users,
>
> Upon was trying to simulate an npt ensemble (protein in water),
> pressure was coupled using  parinello rahman system with tau_p = 2,
> tau_t = 1; compressibility 4.5e-5, type = isotropic.
>
> (cut off scheme (vdw_type = switch; rvdw = 1.0; rvdw_switch = 0.9;
> rcoulomb = 1.2; rlist = 1.2).
>
> No matter what value of tau_p is used (0.5, 1, 2, 2.5, 3, 3.5), the
> pressure
> fluctuations are very drastic. I have gone through the mailing list
> regarding
> this issue but could not come to any conclusion.
>
> Any suggestions are helpfull.
>
> This is one of the statistics for pressure fluctuations.
>
> Statistics over 500001 steps [ 0.0000 through 1000.0000 ps ], 1 data sets
> All statistics are over 100001 points
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Pressure                    5.77629       0.99    398.013   -5.34218  (bar)
>
>
> Looks very normal. See http://www.gromacs.org/Documentation/FAQs number 3
>
> Mark
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