I have been using g_wham, but I have a few questions that I can't find answers to online. When using WHAM, one does not need the forces between the pull groups to calculate the PMF, yet g_wham won't run without it. Is there a reason for this?
I have never used g_wham, but g_wham -h (gromacs-4.0.5) indicates that you are incorrect (see below).
The short answer is probably to use g_wham -h to see that -ix and -if are optional and read the information at the top to see that you should not use both at once.
If you still have problems, please be more explicit like this: "With gromacs version X, I did A (copy text of command here) and I got error message B (copy error message here), and the output file looked like C (copy output file snippit here)... But when I do A2 I get B2, etc."
here is a snippit from g_wham -h : At present, three input modes are supported. * With option -it, the user provides a file which contains the filenames of the umbrella simulation run-input files (tpr files), AND, with option -ix, a file which contains filenames of the pullx mdrun output files. The tpr and pullx files must be in corresponding order, i.e. the first tpr created the first pullx, etc. * Same as the previous input mode, except that the the user provides the pull force ouput file names (pullf.xvg) with option -if. From the pull force the position in the ubrella potential is computed. This does not work with tabulated umbrella potentials. * With option -ip, the user provides filenames of (gzipped) pdo files, i.e. the gromacs 3.3 umbrella output files. If you have some unusual reaction coordinate you may also generate your own pdo files and feed them with the -ip option into to g_wham. The pdo file header must be similar to the folowing:
Also, when using the pull code, I am allowed to define the spring constant K for umbrella sampling, but I do not designate where the umbrella potential is centered. How does gromacs determine this? I am interested as I would like to create a PMF using umbrella integration (from code I will write myself) rather than use WHAM. To do this and still use the umbrella sampling runs used with GROMACS, I need to know where my umbrella potentials are centered.
This is outlined in the online .mdp options section of the manual (again for gromacs 4): http://manual.gromacs.org/current/online/mdp_opt.html#pull
I think everybody agrees that the manual would benefit from some more description about how the pull code works, especially in version 4, but the information that is there should at least get farther than you are now... It's one of those things where the information is all there but this is only obvious once you already understand how it works ;)
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