[gmx-users] microcanonical

karamyog singh karamyog.singh at gmail.com
Thu May 18 10:40:35 CEST 2006

I placed the atoms randomly means i used random atomic positions, not
velocities. The velocities were 0 initially and then I generated velocities
at 0.01 K.(1st MD run to get a stable configuration) After that I subjected
this structure that I got to NVE.(2nd MD run) Now over here I will try with
no velocity generation. Thank you for pointing out this mistake. I should
have realised this. One more thing, is generating velocities in the MD run

I will try what you are saying. I was doing it till the r-min beacuse at
that point the forces become 0.Minimum potential should imply 0 force. So if
the forces are zero and I increase my simulation time for 1st MD run, I get
a stabler structure i.e. the forces between atoms should be nearly equal to
zero. However my forces wil never be zero. Wil I ever get a frozen structure
for NVE?

On 5/18/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> karamyog singh wrote:
> > 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.
> Ah... your .mdp file generated velocities... you don't want to carefully
> equilibrate something, and then put near-random numbers in place of the
> velocities. You just want to turn off the regulation and set gen_vel = no.
> > 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?
> This is certain to be too small. With correctly modeled LJ, you'd expect
> to see a peak in the radial distribution function corresponding to that
> minimum, since all the atoms will be jostling to get there with respect
> to all other atoms - impossible of course, but they'll do it on average
> for their closest neighbours. Here you won't necessarily see that,
> because your effective potential function for all pairs of atoms drops
> from infinity at zero distance to the distance of the minimum value, and
> then to zero.
> Elaborating, as soon as an atom moves to a distance greater than the
> distance of the minimum, they don't interact. The other nearby
> interactions will become more repulsive (if the gas is dense) and
> effectively correct for it, but your effective potential function is not
> LJ any more. Further you say your gas is dilute, so it seems unlikely
> that you have a good physical model... atoms will collide, bounce past
> the minimum distance and have no interactions with anything until they
> collide with another atom. This is not true for an LJ system.
> I'd say you want a cut-off such that the potential at that cutoff is
> approximately zero...
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20060518/9c7b73e1/attachment.html>

More information about the gromacs.org_gmx-users mailing list