On Tue, Jan 28, 2003, vannajan_at_chiangmai.ac.th wrote:
> I did two consecutive calculations, the first one from 1-400ps and then
> 400-800 ps using the restarting file from 400 ps. All the calculations were
> done using Sander with the same input file. I found that the total Energy
> from the first calculation at 400 ps is not the same as what I got from the
> second one. It seems to me that the second one is not the right one.
I think I would need more details to understand your question. You say
that the "total energy from the first calculation at 400 ps is not the same
as what I got from the second one", but I don't understand what you mean
by the phrase "the second one". Can you give a specific example?
Also, the fact that you used the same sander input file doesn't guarantee
it is restarting...you need at least to have irest=1 for the second run.
You can "play" with restarts yourself: run a 20 step simulation, printing
every step. Run 20 steps more, starting from the end of the first one.
Compare that to what you get with a 40 step simulation starting from the
beginning. Having the restart in the middle should make no difference.
It may be that you are just not interpreting the output in the correct
way, and the above exercise could help.
Or, this exercise could help you find some problem with your input files,
or some problem with the Amber code.
..good luck....dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
==================================================================
Received on Mon Jan 27 2003 - 18:33:14 PST
