[gmx-users] Problems with Non-equilibrium MD

Jun Zhou jun.zhou at monash.edu
Tue Mar 17 08:42:46 CET 2020


Hi all,

I am using non-equilibrium MD to calculate the viscosity of the liquid by
applying a shear on xy direction. My problem is that when I observe the
trajectory of the simulation, I find only the box deformed and particles
did not change correspondingly, as shown in the attached image (
https://drive.google.com/file/d/11GJntUJU7-phc-Bz-hWBICvQWFIGUJDI/view?usp=sharing
).

Another question is that when I try to increase the deform rate, there is a
warning: triclinic box is to skewed ... cannot fix pbc. And the simulation
will stop after 1000 steps. How to prevent this?

I also attached my mdp file, can anyone give me some suggestions? Thanks.

Regards,
-- 
*Jun ZHOU*
Postgraduate Student ,
Room 117, Building 36
Department of Civil Engineering,
Monash University,
Victoria 3800, Australia.


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