<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
<META NAME="Generator" CONTENT="MS Exchange Server version 6.5.7654.12">
<TITLE>g_wham output</TITLE>
</HEAD>
<BODY>
<!-- Converted from text/plain format -->
<P><FONT SIZE=2>Dear all,<BR>
<BR>
I have used the PULL code in gmx 4 to unwind part of my protein. 10 runs were performed (all pulling the pulled group from 1.3 nm to 4.3 nm away from the reference). The output seems ok from the pullx.xvg and the trajectories. However, when using g_wham to obtain the PMF there seems to be a problem.<BR>
<BR>
The options for pulling in the mdp file:<BR>
; PULLING STUFF<BR>
pull = umbrella<BR>
pull_geometry = distance<BR>
pull_dim = n y n<BR>
pull_start = yes<BR>
pull_init1 = 0.0<BR>
pull_vec1 = 0.0 1.0 0.0<BR>
pull_rate1 = 0.005<BR>
pull_ngroups = 1<BR>
pull_group0 = Glu33<BR>
pull_group1 = Glu81<BR>
pull_k1 = 5000<BR>
pull_nstxout = 500<BR>
pull_nstfout = 500<BR>
<BR>
Using the command (with all the files where they should be)<BR>
g_wham -ix -it -o -hist<BR>
results in the following:<BR>
@ title "Umbrella potential"<BR>
@ xaxis label "z"<BR>
@ yaxis label "E (kJ mol\S-1\N)"<BR>
@TYPE xy<BR>
1.324382e+00 0.000000e+00<BR>
1.338367e+00 0.000000e+00<BR>
1.352352e+00 0.000000e+00<BR>
1.366337e+00 0.000000e+00<BR>
....<BR>
2.401216e+00 -1.638628e+03<BR>
2.415201e+00 -1.730001e+03<BR>
2.429185e+00 0.000000e+00<BR>
2.443170e+00 -inf<BR>
2.457155e+00 -inf<BR>
2.471140e+00 -inf<BR>
2.485125e+00 -inf<BR>
2.499110e+00 -inf<BR>
2.513095e+00 -inf<BR>
....etc<BR>
<BR>
Using the command (with all the files where they should be)<BR>
g_wham -if -it -o -hist<BR>
results in a more reasonable plot. However, I don't understand what is on the x-axis. I would expect the reaction coordinate (so distance between pulled and reference groups) there, but this doesn't seem to be the case.<BR>
<BR>
I a post of a very similar problem in the mailing list archive of April 2009. It seems, however, that nobody has answered it. I wondered if anyone has a solution to it now?<BR>
<BR>
Thanks,<BR>
Marieke</FONT>
</P>
</BODY>
</HTML>