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.
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