[gmx-users] microcanonical

karamyog singh karamyog.singh at gmail.com
Thu May 18 09:59:08 CEST 2006

I exactly did that. I initially thought that since I have placed the atoms
randomly so it is probable that atoms experience large forces and since I am
not allowing any temperature scaling etc. , I am getting large KE. Therefore
I first minimized my configuration. I got a frozen structure by doing
pressure and temp. scaling. Then I removed everything. After that what
happens is, the whole crystal starts breaking up. First one atom gains
velocity and moves then another atom and then another. After tht the whole
system just breaks.

Any idea why? Is it because the no. of steps for my initial md run is small
. Shall I stabilize my configuration for a longer time?

The cut off that I have taken is the value of 'r' at which the minima for LJ
exists. Is it ok or shall I increase this too?

On 5/18/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> karamyog singh wrote:
> > I almost removed everything. I am generating initial velocity at 0.01 K
> > so the system should freeze. Its a dilute gas. But somehow I am getting
> > very large velocites i.e. very large KE of the whole system.
> That .mdp looks fine for NVE. Use g_energy -w to see the evolution of KE
> over time. It is well known that the use of cut-offs induces heating in
> the system - i.e. energy is not being conserved. Yours are much longer
> than you would use in protein-in-water MD, which is a step in the right
> direction, but I don't know how long they are for the system you're
> looking at - literature may help here. You would want cut-offs that get
> more than a few atoms into the interaction sphere, of course, and that
> depends how dilute the gas is.
> Another possibility is that the system is not equilibrated straight
> after grompp does the gen_vel - it's just sampling velocities from a
> distribution, so the result is stochastic. I'd suggest doing a period of
> NVT and/or NPT to get the temperature and density correct for the system
> you want, and only then switch off the regulation algorithms to get NVE.
> Mark
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