Dear Prof. Spoel, Many thanks for your reply. Since the fourier_n* values are associated with the grid sizing, will these values affect my results drastically? do you suggest resubmitting these runs? regards, Pri...
David van der Spoel <[EMAIL PROTECTED]> wrote: priyanka srivastava wrote: > Hie, > > Many thanks for your reply. > > Yes I have used semi-isotropic coupling. > > Another doubt is why only a value of 4.5e-5? > > I have used PME and have mentioned rcoulomb in the > .mdp file too, which as is pointed out by you, has no > meaning!! But does this mean that my mdp file is > wrong? Because if PME does not use rcoulomb it shud > simply ignore the value. > Actually I do not want to use twin range cutoff. So, I > have given rvdw = rlist. Is this alright? > Portion of my mdp file looks like this: > > ; Electrostatics > coulombtype = PME > fourier_nx = 6.4 > fourier_ny = 5.0 > fourier_nz = 8.1 these numbers should be integers > pme_order = 4 > rcoulomb = 1.5 > rvdw = 1.5 > > Also since I have not specified "vdwtype" in the mdp > file, so it automatically takes Cut-off. > > regards, > Pri... > > > --- Martin H�fling wrote: > >> Am Mittwoch, 20. Juni 2007 schrieb priyanka >> srivastava: >> >>> I am currently involved in doing a lipid-peptide >>> simulation under NPAT conditions. The way I have >>> applied NPAT condition is as follows: >>> >>> ref_p = 0 1 >>> compressibility = 0.0 4.5e-5 >> with semiisotropic? >> >>> Although while performing analysis it shows that >> the x >>> and y dimensions are constant but still I am not >> sure >>> about the way I have applied NPAT. Could somone >> please >>> tell me the basis behind it? >> If i am remembering correctly, this is what above >> values should do: >> >> first dimension is x-y second one is the z >> direction. Reference pressure is 1 >> for both (obviously makes sense) whereas >> compressibility set to 0 for x-y >> plane prevents box changes in x and y direction. So >> only z-direction remains >> for adjusting pressure. >> >>> Another thing is I have used vdwtype: cutoff. >>> But my intention is not to use the twin range >> cutoff >>> at all!! In my case rlist = rcoulomb = rvdw, i.e. >> all >>> three are same!! Is this alright? (the coulombtype >>> = PME) >> Sorry, didn't get that part of your question. Can >> you post relevant parts of >> your mdp and specify it further? Chapter 7 says that >> parameters for PME are >> fourierspacing and pme_order, rcoulomb should not be >> used then. >> >> Cheers >> Martin >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/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/mailing_lists/users.php >> > > > > > ____________________________________________________________________________________ > Pinpoint customers who are looking for what you sell. > http://searchmarketing.yahoo.com/ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php --------------------------------- Get the free Yahoo! toolbar and rest assured with the added security of spyware protection.
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