[gmx-users] PMF calculation using g_wham using different simulation boxes

Li Jianguo ljgsq at yahoo.com
Wed Dec 2 11:06:44 CET 2009

I am trying to calcualte the potential of mean force between two polyatomic particles using umbrella potential and the g_wham command. I need to run multiple windows from close to far inter-particle distance. To save time, I used smaller box sizes for those windows with shorter inter-particle distance, and larger box sizes for those windows with longer inter-particle distance. Then I have multiple pullf files and tpr files with different box sizes. 
I am wondering if using different simulation systems is acceptable when applying g_wham command for PMF calculation.
Thanks in advance,
Li Jianguo
Research fellow
Singapore-MIT Alliance
National University of Singapore

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