<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>Dear All,</span></div><div><span></span> </div><div><span>According to the on-line tutorial on Umbrella Sampling, there is a step to get a lot of configurations, and for each configuration we need to run a MD. For this reaon I regard the Umbrella Sampling method for binding energy calculation is not suitable for relatively large protein complex (I am not sure the MW of the complex used by Justin in the original publication. But for my protein-ligand complex, the total MW is about 50, 000 Dalton), as for the MD for all the configurations will take a rather long calculation time.</span></div><div><span></span> </div><div><span>Do you agree on my view? Or do you have much better
method?</span></div><div><span></span> </div><div><span>Cheers,</span></div><div><span></span> </div><div><span>Acoot</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;"> <div dir="ltr"> <font size="2" face="Arial"> <div style="margin: 5px 0px; padding: 0px; border: 1px solid rgb(204, 204, 204); height: 0px; line-height: 0; font-size: 0px;" class="hr" contentEditable="false" readonly="true"></div> <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> Acoot Brett <acootbrett@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Tuesday, 3 April 2012 8:59 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re:
[gmx-users] on the Umbrella Sampling tutorial<br> </font> </div> <br><br><br>Acoot Brett wrote:<br>> <br>> Dear All,<br>> <br>> For the on-line Umbrella Sampling tutorial "<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/04_EM_equil.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/04_EM_equil.html</a>" of *Justin Lemkul*, will you pleasse tell me for the equilibration where there is no NVT equilibration?<br>> <br><br>It wasn't necessary. The system is quite robust and my experience has indicated that NPT equilibration was sufficient.<br><br>-Justin<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>