Thank you Justin, When I went through most of the mailing list the fluctuations are not so high and even in the FAQ it was mentioned in the range of 500-600 bar for 216 water. And more over the average pressure was ~6bar instead of 1bar which was required.
So would you suggest that I can proceed with this file for the production run without any problem. I was following your lysozyme tutorial where fluctuations were much less.. hence I suspected some problem in this data. Thanking you With regards M. Kavyashree On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Kavyashree M wrote: > >> 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? >> > > No. It is entirely expected, as you've been told. Also pay attention to > this statement from the page linked before: > > "How much it varies and the speed at which it does depends on the type of > pressure coupling used and the value of the coupling constants." > > You may not see the exact same behavior described on the Pressure page if > you're using different settings. > > There is no problem here. > > -Justin > > 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.abra...@anu.edu.au<mailto: >> mark.abra...@anu.edu.au>> wrote: >> >> >> >> On 16/03/11, *Kavyashree M * <hmkv...@gmail.com >> <mailto:hmkv...@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 >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> 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 gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists