Hi,<br><br>I ran g_wham 4.5.2 and did get a non-zero PMF curve. <br>I assume that there is something going on with g_wham on version 4.5.1.<br><br>Thank you for your help.<br><br>Susana<br><br><div class="gmail_quote">On Wed, Mar 9, 2011 at 3:00 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div text="#000000" bgcolor="#ffffff"><div class="im">
On 10/03/2011 1:43 AM, Susana Tomasio wrote:
<blockquote type="cite">Thank you Jianguo.<br>
<br>
So can I use g_wham 4.5.2 even though I ran the simulations on
4.5.1?<br>
</blockquote>
<br></div>
Quite likely. Check the change logs on the GROMCACS website for
relevant issues.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite"><br>
Best regards,<br>
<br>
Susana<br>
<br>
<br>
<br>
<div class="gmail_quote">On Wed, Mar 9, 2011 at 2:31 PM, Jianguo
Li <span dir="ltr"><<a href="mailto:ljggmx@yahoo.com.sg" target="_blank">ljggmx@yahoo.com.sg</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">
<div>I met the same problem when using 4.5.1 for some
systems, the PMF shows zero curve, while the hist file
looks fine. The problem disappears when using 4.5.2.</div>
<div>Jianguo<br>
</div>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2">
<hr size="1">
<b><span style="font-weight: bold;">From:</span></b>
Susana Tomasio <<a href="mailto:susietomasio@gmail.com" target="_blank">susietomasio@gmail.com</a>><br>
<b><span style="font-weight: bold;">To:</span></b> <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<b><span style="font-weight: bold;">Sent:</span></b>
Wednesday, 9 March 2011 20:07:25<br>
<b><span style="font-weight: bold;">Subject:</span></b>
[gmx-users] Zero Potential of Mean Force with g_wham<br>
</font>
<div>
<div><br>
Dear all,<br>
<br>
I am running umbrella sampling of a molecule
through a lipid bilayer with gromacs 4.5.1.<br>
When I extracted the potential of mean force with
g_wham I got zero for all the windows.<br>
Any ideas of why this is happening?<br>
<br>
This is the command I used: <br>
g_wham_4.5.1 -it tpr.dat -if pullf.dat -o -hist<br>
<br>
And this is the pull code of my .mdp file:<br>
<br>
; Pull code<br>
pull = umbrella <br>
pull_geometry = position <br>
pull_dim = N N Y <br>
pull_start = yes <br>
pull_ngroups = 1 <br>
pull_group0 = Bilayer <br>
pull_group1 = Protein <br>
pull_vec1 = 0 0 0 <br>
pull_init1 = 0 0 0 <br>
pull_rate1 = 0 <br>
pull_pbcatom0 = 1453 <br>
pull_pbcatom1 = 13187 <br>
pull_k1 = 3000 ; kJ mol^-1 nm^-2<br>
pull_nstxout = 1000 ; every 2 ps<br>
pull_nstfout = 1000 ; every 2 ps<br>
<br>
Thank you.<br>
Best regards,<br>
<br>
Susana<br>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
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