Thanks, You should make sure your WHAM is good, or your DNA isnt moving out of the box, as I watched a series of questions reply here before which showed that irrelevant WHAM data might be produced when the molecule leaves the box edges, ie you would be missing a piece or have a negative where the positive number should be in the calculations used inside WHAM.
Grüess Stephan -------- Original-Nachricht -------- > Datum: Mon, 25 Jun 2012 02:32:40 -0700 (PDT) > Von: anaome <[email protected]> > An: [email protected] > Betreff: [gmx-users] Re: umbrella sampling with distances larger than half > box size > Thanks Stephan for your suggestions, > > A finally found a solution for distance larger than half the box size: > 1) Regenerate the tpr files with pbc=no > 2) Perform WHAM analysis with the umbrella forces (-if) > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/umbrella-sampling-with-distances-larger-than-half-box-size-tp4998779p4998782.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 -- NEU: FreePhone 3-fach-Flat mit kostenlosem Smartphone! Jetzt informieren: http://mobile.1und1.de/?ac=OM.PW.PW003K20328T7073a -- 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
