[gmx-users] "comm-mode = Angular" gives error

[Justin Lemkul]

On 8/20/19 5:21 AM, Jorden Cabal wrote:
> Hi Justin,
> Thank you for your response. In my case the cost of increasing simulation
> box is very large. I have already tried it by keeping distance between the
> periodic images of the macromolecule up to 50 Angstrom. Could you suggest
> me any other option to do this. In Gromacs, rotation around pivot can be
> enforced, is it possible to use this method somehow to counter the
> rotation? Even if its possible, how and to which extent do you think it
> will add biasness to the independent behavior of the macromolecule. Any
> suggestions, comments in this regard will help me.

You can apply biasing potentials to avoid rotation, but then you're 
seriously perturbing the dynamics in a way that might completely bias 
your results (I don't have nearly enough context to say for sure, so 
I'll be a bit circumspect). If you have a large molecule that rotates, 
you need a large box that reflects that intrinsic symmetry. It's the 
same reason you can't build a long, rectangular box around a DNA duplex. 
If it rotations orthogonal to the longest axis, it sees it's image and 
the forces are invalid.

There are no real "tricks" here. If you have a big molecule, you need a 
suitably large box.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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