Ah, now I see what you meant. Then it is fine. That is a separate issue and is not really a problem for me.
Thank you, Ondrej On Tue, Nov 24, 2009 at 17:39, Berk Hess <[email protected]> wrote: > Hi, > > Sure g_rdf takes care of pressure coupling, but the cut-off of the rdf plot > is set from the initial frame. > So if your volume fluctuates a lot, you might have incorrect normalization > very close to the cut-off. > But in "normal" liquid simulations the box length will never change more > than 1%. > > Berk > >> Date: Tue, 24 Nov 2009 17:12:44 +0100 >> Subject: Re: [gmx-users] Normalization in g_rdf >> From: [email protected] >> To: [email protected] >> >> Hi again, >> >> I thought pressure coupling is handled by g_rdf. Looking at the code, >> it seems that the block starting with: >> >> /* Must init pbc every step because of pressure coupling */ >> >> takes care of that, so even with a relatively big volume change at the >> beginning, it should not be a problem. Is that not the case? >> >> Ondrej >> >> >> On Tue, Nov 24, 2009 at 16:12, Berk Hess <[email protected]> wrote: >> > Hi, >> > >> > g_rdf limits the distance to half the minimum periodic image distance. >> > So the volume normalization is always simply 4 pi r^2. >> > It uses the starting unit-cell with a factor of 0.99. >> > So you would only see strange effects when the box length reduces >> > more than 1% due to pressure coupling. >> > >> > Berk >> -- >> gmx-users mailing list [email protected] >> http://lists.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 > > ________________________________ > New Windows 7: Simplify what you do everyday. Find the right PC for you. > -- > gmx-users mailing list [email protected] > http://lists.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 > -- gmx-users mailing list [email protected] http://lists.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
