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.
Mark
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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