We'd need to see your output file here to get an idea of what is going on.
The energy increasing could be suggestive of a bad starting structure. Again
seeing the output will help.
As for converging the minimiser will either run until:
1) MAXCYC is exceeded.
2) Too many LINMIN failures.
3) RMS target is achieved.
In all 3 cases a message should be written to the output file explaining why
the minimisation run is stopping.
All the best
Ross
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Gustavo Pierdominici Sottile
Sent: 09 February 2005 09:36
To: amber.scripps.edu
Subject: AMBER: energy plot in minimization
Hi,
There is something rare in the plot of the energy when doing a
minimization. At first the energy oscilates and then there is an abrupt
decrease when the method changes. Afterwards, the energy goes up. This rise
keeps on and then it seems to arrive to a plateau.
I will not do a normal mode analysis, but I donīt understand why it
increases.
Another doubt is to know if the convergence criterion is achieved or not.
Perhaps the anwser is that the ending has less steps than "maxcyc"
Thanks
Gustavo
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Received on Wed Feb 09 2005 - 18:53:00 PST
