[gmx-users] Simulating crystalls

karamyog singh karamyog.singh at gmail.com
Mon May 29 10:31:29 CEST 2006

However if the gen_velocity breaks up my system and at the end of my
simulation, I do not get a bcc structure at lets say 273 K, which I am not
getting, then how can I consider my simulation to be correct? The structure
should remain the same. Or could it be that since my structure is a nano
layer film, therefore it is unstable and explodes and I should not compare
my results with a bulk material?

Moreover, to avoid the error in the LJ, I have changed my system to copper
and have used the potential parameters given in gromacs. Temperature of
simulation is 273 and I have used the option no for Pressure coupling
because i want my system to be at 1 bar.

On 5/29/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> karamyog singh wrote:
> > Does this give any clue. It shows large PE, KE and temp. Could that be a
> > reason? More information required?
> Your PE is ridiculously large. You have order 10^5 kJ/mol of PE for
> every atom, and obviously that is only coming from your LJ function.
> Check how you generated that and told gromacs what it should be. Be
> careful of units and multiples of 1000! In the absence of temperature
> control, that PE will equipartition to the KE degrees of freedom,
> leading to the other observations of high KE and temperature.
> > However, I have chenged my system a bit. My conf.gro file has just 2
> > atoms. one at the origin and the other at the body center. I use genconf
> > to create a mesh of 4x4x4 unit cells at a distance of 0 0 0.  I thought
> > this is a better way to simulate a set of crystals.
> Sounds like a better way to generate your simulation cells. You
> shouldn't now have overlapping atoms (check the output .gro file
> yourself) but you will have a simulation cell that is initially
> symmetric, until the gen_vel random KE breaks it.
> Mark
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