Hi, Jochen, Thanks a lot for your reply. I looked at the example header provided by g_wham -h. I just wonder if you can answer some more questions for me.
The example header is # UMBRELLA 3.0 # Component selection: 0 0 1 # nSkip 1 # Ref. Group 'TestAtom' # Nr. of pull groups 2 # Group 1 'GR1' Umb. Pos. 5.0 Umb. Cons. 1000.0 # Group 2 'GR2' Umb. Pos. 2.0 Umb. Cons. 500.0 ##### I guess following "# Component selection" one need to specify the Cartesian coordinate components in which the distance restraints are applied. In this example, I guess the restraint is applied in the Z coordinate, right? If, say, I want to put restraints in all three coordinates, X,Y, and Z, I need to put "1 1 1" here, right? In this case, there shall be 3 coordinates to specify the Umb. Pos., so I would put something like "# Group 1 'GR1' Umb. Pos. 5.0 5.0 5.0 Umb. Cons. 1000.0", assuming the force constant is same for X, Y, and Z. Am I right, or is there some other way to specify the position of the umbrella? And I should have 1 time column and 3 data columns/per-group following the headers, right? If, instead of using the pull code, I create by hands a set of initial configurations where the pull-groups are placed along a curved pathway, and use "pull_start = yes" with "pull_rate1 = 0", will GROMACS and g_wham automatically recognize the positions of the umbrellas from the initial configurations? Thank you very much! Hao On Thu, Feb 16, 2012 at 10:42 AM, Jochen Hub <[email protected]> wrote: > Hi, > > since there is no pull type for curved pathways, you have to generate the > gmx3-type pdo files from your simlation output and use these in g_wham > (g_wham -ip). See g_wham -h for a example header of a pdo file. > > Cheers, > Jochen > > > > Am 2/14/12 5:53 PM, schrieb HAO JIANG: > >> Dear all, >> >> I would like to calculate the PMF along a curved reaction pathway >> using umbrella sampling. I just wonder if it is appropriate to use >> g_wham to extract the PMF along the curved pathway? Any help would be >> appreciated. >> >> Hao Jiang > > > -- > --------------------------------------------------- > Dr. Jochen Hub > Computational Molecular Biophysics Group > Institute for Microbiology and Genetics > Georg-August-University of Göttingen > Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany. > Phone: +49-551-39-14189 > http://cmb.bio.uni-goettingen.de/ > --------------------------------------------------- > -- > 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 -- 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
