[gmx-users] Umbrella Sampling - Loop Motion
Michael.Carter at icr.ac.uk
Tue Nov 11 12:21:17 CET 2014
I am setting up an umbrella sampling simulation to analyse the motion of a loop within my protein system.
I have set it up so that the pull groups are:
1 – the loop (residues 208-14)
2 – the protein (protein)
However, when doing this my conformations which I generate in the md_pull step are very strained. Is this because I am also including the loop in the 2nd pull group (defined as protein)?
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