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><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">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></div>
<div class="h5"><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><br>--<br>
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