[gmx-users] Umbrella_pull_simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 24 15:10:24 CET 2012

shahid nayeem wrote:
> My system is a  protein-protein complex. After pulling I selected 
> windows at 0.1nm from an initial COM distance of 3.65nm to 5.7nm and 
> thereafter windows at 0.2nm spacing was selected  upto 7.5nm. In each 
> window 10ns MD was done and g_wham command was run neglecting the fist 
> 1ns run for equilibriation.

OK, so how did you decide that 10 ns was sufficient in each window?



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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