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<DIV><FONT face=Arial size=2>Dear gmx users,</FONT></DIV>
<DIV><FONT face=Arial size=2>my goal is to aquire a PMF courve of two
amino-acids (ASP and LYS) of which one is pulled from the other. I followed
Justin's tutorial on umbrella sampling.</FONT><FONT face=Arial
size=2></FONT></DIV>
<DIV><FONT face=Arial size=2>Here are the results.</FONT></DIV>
<DIV><FONT face=Arial size=2>profile.xvg:</FONT></DIV>
<DIV><FONT face=Arial size=2><A
href="http://przemekbartha.pl/upload/profile.png">http://przemekbartha.pl/upload/profile.png</A></FONT></DIV>
<DIV><FONT face=Arial size=2>histo.xvg:</FONT></DIV>
<DIV><FONT face=Arial size=2><A
href="http://przemekbartha.pl/upload/histo.png">http://przemekbartha.pl/upload/histo.png</A></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I would be grateful, if anyone could tell me why is
the PMF so irregular, unstable, unlike the courve in the tutorial:</FONT></DIV>
<DIV><FONT face=Arial size=2><A
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/07_analysis.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/07_analysis.html</A></FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>After a little bit of research on "gmx-users", my
guess is either incorrent sampling or/and some major mistake in
parametrization.</FONT></DIV>
<DIV><FONT face=Arial size=2>I tried to resample the simulation so that the
"umbrellas" don't overlap as much as they do in my histo.xvg file but it
changed the PMF totaly and did not resolve the problem.</FONT></DIV>
<DIV><FONT face=Arial size=2>Or maybe, it is just the way it should
be?</FONT></DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2></FONT></SPAN> </DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2>My pullcode is nearly the same as in
the tutorial. I don't want to trash, but if you require any additional
information, please let me know.</FONT></SPAN></DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2>The sampling is twice as small as in
the tutorial since my computational resources are limited, but when I tried
running more precise sampling, the results were pretty much the same (irregular
courve).</FONT></SPAN></DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2></FONT></SPAN> </DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2>Thanks in advance.</FONT></SPAN></DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2>Przemek</FONT></SPAN></DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2></FONT></SPAN> </DIV>
<DIV><SPAN lang=P><FONT face=Arial size=2></FONT></SPAN> </DIV>
<DIV><SPAN lang=P><SPAN lang=P><FONT face=Arial size=2>part of
md_umbrella.mdp:</FONT></SPAN></SPAN></DIV>
<DIV><SPAN lang=P><SPAN lang=P><FONT face=Arial
size=2></FONT></SPAN></SPAN> </DIV>
<DIV><SPAN lang=P><SPAN lang=P>; Run parameters<BR>integrator = md<BR>dt =
0.004<BR>tinit = 0<BR>nsteps = 2500000 ; 10 ns </DIV></SPAN></SPAN>
<DIV><SPAN lang=P>; Pull code <BR>pull = umbrella<BR>pull_geometry =
distance<BR>pull_dim = N N Y<BR>pull_start = yes <BR>pull_ngroups =
1<BR>pull_group0 = Chain_B <BR>pull_group1 = Chain_A <BR>pull_init1 =
0<BR>pull_rate1 = 0.0<BR>pull_k1 = 1000 ; kJ mol^-1 nm^-2<BR>pull_nstxout = 1000
; every 2 ps<BR>pull_nstfout = 1000 ; every 2
ps</DIV></SPAN></FONT></DIV></BODY></HTML>