[gmx-users] Umbrella Sampling - Loop Motion

[Michael Carter]

Hi,

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)?

Thanks,

Michael


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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