[gmx-users] Problems with AFM pulling

Tue Apr 18 10:12:35 CEST 2006

&nbsp;&nbsp;&nbsp;Hello,everyone
&nbsp;&nbsp;&nbsp; &nbsp;I am trying to simulate the pulling process of a protein by Gromacs 3.2.0. However, when executing the command "mdrun -v -s pull.mdp -o pull_1.tpr -c afterpull -pi pull.ppa -pn pull.ndx", the program only back off the pullout.ppa and pull.pdo with no computing done. &nbsp;&nbsp;&nbsp; I don't know what's the reason. Is there some problem with my pull.ppa file? Content of the file is:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; verbose&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = no&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; runtype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = afm&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; group_1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = Pull_C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; reference_group&nbsp;&nbsp;&nbsp; = Pull_N&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; reftype&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = com&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; pull_dim&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = N N Y
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; afm_rate1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 0.001 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; afm_k1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 1000&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; afm_dir1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 0.0 0.0 1.0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; afm_init1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 0.0 0.0 0.0&nbsp;&nbsp; Thanks for any message.
--
USTC Alumni Email System 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060418/38418190/attachment.html>