On Fri, Oct 02, 2020, Ari Zeida wrote:
>
>I have performed MD simulations on a trimeric protein complex (let's say
>protein A, B and C). I have run the simulations using the iwrap=1 option.
>At a certain point of the dynamics, part of the C protein "got out of the
>box", and now I'm having trouble imaging the resulting trajectories using
>cpptraj. I've tried centering in a sequential way, first protein A, then
>A-B, then A-B-C (that worked for me in the past) without good results. I've
>also followed without success Dan Roe suggestions posted in
This is a very old (2012) post from Dan, and I suspect there are better
ways to handle this now. Consider using the "unwrap" option prior to
imaging.
And, for the future, avoid iwrap=1.
[Developers: what about adding something like an "expert_mode" variable
to the cntrl namelist? Users would have to set "expert_mode=.true." to
allow access to variables like iwrap, that generally should be avoided
except in special situations?]
....dac
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Received on Fri Oct 02 2020 - 09:00:04 PDT
