[gmx-users] microcanonical

karamyog singh karamyog.singh at gmail.com
Thu May 18 18:14:54 CEST 2006

Well, I am back. Remember my first and second mdruns. In my second, after
stablizing my initial configuration in the 1st md run, I used cut off upto
6.3 whereas the potential minima is at 0.309. 6.3 is quite large a distance
compared to 0.309.  In the second run, the kinetic energy increases which is
correct but the total energy doesnt seem to remain constant even when there
are 3 million steps involved.

How is this constant energy mode? KE increases(accepted) but the total never
seems to be constant. I cant keep increasing my no. of steps. moreover how
can so many vibrations be introduced at a temp. of 0.001 K.

I stabilized the initial configuration using 2 million steps so that there
is less error.

Please help :(

On 5/18/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> karamyog singh wrote:
> > I know where the minimum is and I said exactly what you did. However I
> > interpreted the potential becoming 0 as the point before r-min. The
> > potential once becomes 0 before minimum potential value. I thought you
> > were referring to that point and that is why i got confused and asked
> > you further questions.
> Yes, you want a cut-off such that both U and dU/dx approximates 0 :-)
> Mark
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