[gmx-users] Umbrella Sampling - Loop Motion

Michael Carter 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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