OK, what if I have only one dimension (end-to-end distance), is there any way to do that in GROMACS, or is the best way to just write a little app for myself?
Warren Gallin On 2010-06-23, at 11:29 AM, Justin A. Lemkul wrote: > > > Warren Gallin wrote: >> Hi all, >> I am trying to use g_sham to generate a free-energy profile based on >> the end-to-end distances of a peptide. >> The only documentation that I have been able to find is in the GROMACS >> v.4 pdf manual, which is a little out-of-date, and the g_sham -h output, >> which I assume is the most current. >> My input file (dist_div.xvg) is a simple list of distances, one per >> line, stripped out of the g_dist output from a trajectory. >> The command line is: >> g_sham -f dist_div.xvg -notime -ls Free.xpm -dist energy_dist.xvg -histo >> histogram.xvg -xvgr >> The program runs without errors or warnings, but: >> 1) There is no Free.xpm or histogram.xvg file written >> 2) The file energy_dist.xvg does not have any of the expected legend code, >> it is only the data for bin number vs. Energy >> 3) The bin sizes do not seem to be correct i.e. when I divide the difference >> between the largest number and the smallest number by 32, and then check the >> expected boundary values for bin 0 and bin 31, I find lengths in the wrong >> bins >> Can anyone give me some insight into the actual workings of g_sham and >> what I might be doing wrong (or incorrectly expecting) here? > > Your input file is incorrect. In order to generate a 2-D free energy > surface, you need to feed g_sham two variables. The format of the input .xvg > file needs to be one of two options: > > 1. with time > > time value1 value2 > > 2. without time > value1 value2 > > The difference can be interpreted by g_sham -[no]time, depending on your > preference. > > -Justin > >> Warren Gallin >> > > -- > ======================================== > > 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/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/mailing_lists/users.php > -- 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/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/mailing_lists/users.php
