<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Hi Justin,</span></div><div><span>If you observe my pulling simulation, you will see that the distances are (increasing) in the negative. <br></span></div><div><span><br></span></div><div><span>Here is the PMF (image):<br></span></div><div><span>http://www.flickr.com/photos/nahrenmascarenhas/6312990056/</span></div><div><span>this is not one expects in ligand unbinding. (of course these are from my initial simulations, approx. 1 ns runs in 5 windows)<br></span></div><div><br><span></span></div><div><span>Best,</span></div><div><span>nahren<br></span></div><div><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Arial" size="2"><hr size="1"><b><span style="font-weight:
bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> nahren manuel <meetnahren@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Friday, November 4, 2011 7:44 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] PMF when pulling in -Z direction<br></font><br><br><br>nahren manuel wrote:<br>> Dear Gromacs Users,<br>> <br>> I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx 4.5.3). during my initial pull to generate configurations for umbrella windows I have pulled in the -Z direction,<br>> @ s0 legend "0 Z"<br>> @ s1 legend "1 dZ"<br>> 0.0000 7.37361 -0.33625<br>> 0.0200 7.37377 -0.33631<br>> 0.0400 7.37404 -0.33637<br>> 0.0600
7.3744 -0.33643<br>> 0.0800 7.37473 -0.33649<br>> .<br>> .<br>> .<br>> .<br>> 321.0800 7.37523 -1.29949<br>> 321.1000 7.37442 -1.29955<br>> 321.1200 7.37374 -1.29961<br>> 321.1400 7.37355 -1.29967<br>> 321.1600 7.37404 -1.29973<br>> 321.1800 7.37491 -1.29979<br>> 321.2000 7.3757 -1.29985<br>> 321.2200 7.37608 -1.29991<br>> 321.2400 7.37595 -1.29997<br>> 321.2600 7.37518 -1.30003<br>> 321.2800 7.37395 -1.30009<br>> .<br>> .<br>> .(so on)<br>> <br>> Now when I ran simulations in each umbrella windows, the PMF energies are in negative. My guess is that this is due to my
initial setup, or is there something seriously wrong. And if i am right I should get the correct PMF by taking the negative of this PMF (or is it)??<br><br>So your PMF is negative, why is that a problem? A negative binding energy indicates favorability of binding.<br><br>-Justin<br><br>> -----<br>> ; Pull code (pulling simulation)<br>> pull = constraint<br>> pull_geometry = distance pull_dim = N N Y<br>> pull_start = yes pull_ngroups = 1<br>> pull_group0 = Protein<br>> pull_group1 = MAL<br>> pull_rate1 = 0.005 ;<br>> pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>> pull_nstxout = 500 ; every 1
ps<br>> pull_nstfout = 500 ; every 1 ps<br>> <br>> -----<br>> <br>> ; Pull code (Umbrella simulation)<br>> pull = umbrella<br>> pull_geometry = distance ;<br>> pull_dim = Y Y Y<br>> pull_start = yes ;<br>> pull_ngroups = 1<br>> pull_group0 = Protein<br>> pull_group1 = MAL<br>> pull_rate1 = 0.000 ;<br>> pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>> pull_nstxout = 500 ; every 1 ps<br>> pull_nstfout = 500 ; every 1 ps<br>> <br>> <br>> Best,<br>> nahren<br>> <br>> <br>> <br>> <br>>
<br>> <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br><br><br></div></div></div></body></html>