[gmx-users] Simulating crystalls
karamyog.singh at gmail.com
Mon May 29 10:42:58 CEST 2006
I am sorry.My system does not explode. It just kind of fuses. The atoms come
close together and form a rounded mass.
On 5/29/06, karamyog singh <karamyog.singh at gmail.com> 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. 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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