[gmx-users] Simulating crystalls

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 29 09:53:48 CEST 2006

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.


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