<br><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
Michael McGovern wrote:<br>
> Hi everyone. I'm having some trouble using g_wham to analyze some<br>
> results. I have some simulations from gromacs 3.3 using the pull<br>
> code. I'm using the latest version of g_wham to analyze the results,<br>
> which the help file says is ok, using the -ip option.<br>
><br>
> I've gotten almost everything to work, and it generates histograms<br>
> that seem perfectly reasonable, but sometimes the free energy it<br>
> outputs is completely flat, with each bin having a free energy value<br>
> of 0.<br>
><br>
> I've played around with the -b and -e options using only part of my<br>
> data, and sometimes it gives non-flat free energies, other times not.<br>
> I see no logic to when it works and when it doesn't. My data does<br>
> have good overlap of the histograms, and it sometimes converges even<br>
> when I use data that have no overlaps, so that doesn't seem to be the<br>
> problem.<br>
><br>
> I'm completely confused. Does anyone know what could cause this?<br>
><br>
><br>
<br>
Hi Micheal,<br>
<br>
how large is your data? Could you send me a tar.gz of your pdo files? I<br>
would like to make sure that there is no bug in g_wham.<br>
<br>
Jochen<br>
<br></blockquote></div><br>I had this problem also when I tried to calculate dimerization free energies using umbrella sampling and g_wham. The problem seemed to occur every time I included .tpr files that contained configurations in which there were no more interaction between the previously dimerized set. What I mean is, when I monitored the LJ and Coul interactions between my molecules, I found out that there would be no more interaction beyond, lets say, 2.1 nm (distance between COM of my molecules). When I included the 2.0, 2.1, 2.2 nm etc windows in my g_wham analysis, I got a flat free energy graphic.<br>
Just wanted to add that to the post.<br>Thanks<br>