From: Dong Luo (us917_at_yahoo.com)
Date: Fri Jul 29 2011 - 14:36:44 CDT
Re-minimize the system before restart worked around the problem. But I am not sure how the results will be affected by the reinitialization of atom speed.
From: Dong Luo <us917_at_yahoo.com>
To: namd-l list <namd-l_at_ks.uiuc.edu>
Sent: Thursday, July 28, 2011 1:21 PM
Subject: namd-l: "Constraint failure in RATTLE algorithm" when restart FEP
The FEP simulation is on a mutation from TYR to ALA. The mutated residue is surround by other residues. Upon continue from restart files, the simulation immediately complained with "ERROR: Constraint failure in RATTLE algorithm for atom ####". Check the protein in VMD show that some of the TYR atoms are within 1 angstrom of atoms from surrounding residues. Is this normal as TYR is disappearing during the simulation? But how can a restart get over with that ERROR. It looks to me the simulation runs without problem before the restart point with the same situation. The configuration file for restart is following previous posts in this mailing list.
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