[gmx-users] Average crystallographic angles for a triclinic box
Lakshman Ji Verma
lakshmanjivrm at gmail.com
Tue Nov 20 02:36:17 CET 2018
Thanks, Justin, I was thinking the same about isotropic pressure. As we
applying the same pressure from all directions, there would be only normal
stress and imbalance in normal stress will manifest in the change in box
length. Therefore the angles should not fluctuate. If what I am thinking is
correct, it makes me ask a couple of followup question regarding
When we apply anisotropic pressure, we effectively apply shear, aren’t we?
Also if we use the same pressure in all direction with anisotropic
barostat, it will be the same as isotropic, right? If not, why?
On Mon, Nov 19, 2018 at 5:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
> > done isotropic NPT simulations without restrains.
> > I want to calculate the box length and angle (alpha, beta, gamma) to
> > 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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