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 <[email protected]>wrote: > > > On 16/03/11, *Kavyashree M * <[email protected]> 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 > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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