[gmx-users] Scale Triclinic Box

[Justin Lemkul]

On 4/3/20 11:16 PM, Maryam Sadeghi wrote:
> Hi Salman,
>
> Tnx for the info, I actually want to do the cold-compression on my
> crystalline structure. So basically I need to both compress and expand the
> a and b parameters of the unit cell (the c parameter is already
> optimized)... so it's not just building a supercell, but rather scaling
> only 2 parameters of the unit cell simultaneously while remaping the new
> coordinates inside the scaled cell... could "gmx  genconf -nbox ... ...
> ..." handle this?

It sounds like you need to actually perform a simulation in which high 
pressure is applied to compress the box. genconf is for duplicating a 
box N times in each dimension, and while you can change box vectors and 
scale coordinates with editconf (-scale option), this is not the same as 
compressing them and bond lengths, etc. will become distorted.

-Justin

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Justin A. Lemkul, Ph.D.
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