[gmx-users] Concerns with g_wham

[chris.neale at utoronto.ca]

> 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 ;)

Chris.