[gmx-users] Simulating crystalls

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 29 10:38:36 CEST 2006

karamyog singh wrote:
> 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. 

I don't get the impression you read my post. I don't have to spend my 
time helping you :-) I think gen_velocity is not breaking the system, 
your LJ potential is breaking the system because energy is flowing from 
PE to KE. See my post below again.

> 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?

I wouldn't know.

> 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.

That just gives you NVT or NVE, not NPT or NPE with P=1 bar. You would 
only have a pressure of 1 bar there if you did so by construction.


>     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.

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