<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><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 size=2 face=Tahoma>
<HR SIZE=1>
<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Susana Tomasio <susietomasio@gmail.com><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> gmx-users@gromacs.org<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><BR>
<META content=off http-equiv=x-dns-prefetch-control>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>
<META content=on http-equiv=x-dns-prefetch-control></DIV></DIV></div><br></body></html>