From: Shirley Li (li19104_at_yahoo.com)
Date: Sat Dec 24 2005 - 12:58:55 CST
Dear NAMD experts,
After finishing mimization, I tried running heating the system, but got the following message from heating:
ERROR: Constraint failure in RATTLE algorithm for atom 29326!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely
I checked the minimized structure, the atom 29326 and the corresponding residue are too far from its two neighboring residues, just as what the related messages in NAMD archive suggested. The number of steps for the minimization was 26000 for fix-backbone MIN + 6000 for restraint-free MIN. I'm thinking of increasing them to 56000 + 26000 respectively. I have some questions here:
1) Is it possible to solve this problem by extending the minimization?
2) Are 56000 +26000 steps too long?
3) Is there any other better way for this problem?
Your help will be greatly appreciated.
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