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 correct?<br>
<br>
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?<br><br>
-<br>
karamyog.<br><div><span class="gmail_quote">On 5/18/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
karamyog singh wrote:<br>> I exactly did that. I initially thought that since I have placed the<br>> atoms randomly so it is probable that atoms experience large forces and<br>> since I am not allowing any temperature scaling etc. , I am getting
<br>> large KE. Therefore I first minimized my configuration. I got a frozen<br>> structure by doing pressure and temp. scaling. Then I removed<br>> everything. After that what happens is, the whole crystal starts
<br>> breaking up. First one atom gains velocity and moves then another atom<br>> and then another. After tht the whole system just breaks.<br><br>Ah... your .mdp file generated velocities... you don't want to carefully
<br>equilibrate something, and then put near-random numbers in place of the<br>velocities. You just want to turn off the regulation and set gen_vel = no.<br><br>> Any idea why? Is it because the no. of steps for my initial md run is
<br>> small . Shall I stabilize my configuration for a longer time?<br>><br>> The cut off that I have taken is the value of 'r' at which the minima<br>> for LJ exists. Is it ok or shall I increase this too?<br>
<br>This is certain to be too small. With correctly modeled LJ, you'd expect<br>to see a peak in the radial distribution function corresponding to that<br>minimum, since all the atoms will be jostling to get there with respect
<br>to all other atoms - impossible of course, but they'll do it on average<br>for their closest neighbours. Here you won't necessarily see that,<br>because your effective potential function for all pairs of atoms drops<br>
from infinity at zero distance to the distance of the minimum value, and<br>then to zero.<br><br>Elaborating, as soon as an atom moves to a distance greater than the<br>distance of the minimum, they don't interact. The other nearby
<br>interactions will become more repulsive (if the gas is dense) and<br>effectively correct for it, but your effective potential function is not<br>LJ any more. Further you say your gas is dilute, so it seems unlikely<br>
that you have a good physical model... atoms will collide, bounce past<br>the minimum distance and have no interactions with anything until they<br>collide with another atom. This is not true for an LJ system.<br><br>I'd say you want a cut-off such that the potential at that cutoff is
<br>approximately zero...<br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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