Thank you Justin! On Wed, Mar 16, 2011 at 9:28 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Kavyashree M wrote: > >> 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. >> > > You cannot always assume that rules of thumb and others' results will (or > should) necessarily match your own. Unless you are using identical input > files, you won't necessarily get the same results. Much of the fluctuation > information is probably based on the Berendsen thermostat, which does not > oscillate as much as Parrinello-Rahman. Other factors in the .mdp file will > influence these statistics, since both the kinetic energy of the system and > the virial are used to calculate pressure (see the manual). > > > And more over the average pressure was ~6bar instead of 1bar which was >> required. >> >> > And with fluctuations +/- 1000, is 6 really all that different from 1? > There was an extensive discussion some time back about this. I would > suggest you have a look through the archive. > > > 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. >> >> > The lysozyme system has nearly twice the number of waters that your system > has (over 10,000), hence the fluctuations will be much smaller, and even > then, the pressure oscillates by +/- 400 or so. > > Again, I see no problem here. What you report is what is to be expected. > > -Justin > > Thanking you >> With regards >> M. Kavyashree >> >> >> On Wed, Mar 16, 2011 at 8:52 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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> >> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- 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 >
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