[gmx-users] Average crystallographic angles for a triclinic box

Justin Lemkul jalemkul at vt.edu
Tue Nov 20 00:52:53 CET 2018

On 11/19/18 5:42 PM, Lakshman Ji Verma wrote:
> Hi all,
> I am trying to validate a force field (ff) for a crystal structure. I have
> done isotropic NPT simulations without restrains.
> I want to calculate the box length and angle (alpha, beta, gamma) to check
> the validity of the ff. I found one similar thread but it doesn't answer
> my question.

If you use isotropic coupling, the angles between the box vectors can't 
change, so they stay at whatever you've set them to at the outset of the 
simulation. If you are working with a crystal, anisotropic coupling may 
be more appropriate as this will be a proper test of the force field, 
since the box can actually deform.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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