From: Shirley Li (li19104_at_yahoo.com)
Date: Tue Dec 27 2005 - 12:28:52 CST
Thanks Dimka so much for the kind and quick help. That's very helpful to me. I fixed the structure before minimization instead of simply extending the MIN, now the MIN and heating run smoothly.
Have a happy holiday season.
dimka <newyorkdimka_at_gmail.com> wrote: Hi Shirley,
The atoms you're talking about may be "tangled". If that is the case, you can use VMD's move atom/residue option to help bring the atom in the right proximity.
When you plot the energies from NAMD log you'll see that this value converges or reaches a plateau at some point. From experience, it takes about 300-2000 steps to reach that point. Increasing the number of steps won't do much.
Yahoo! for Good - Make a difference this year.
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