[gmx-users] Simulating crystalls
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.
More information about the gromacs.org_gmx-users