From: Corey Fugate (coreyfugate_at_gmail.com)
Date: Mon May 20 2013 - 11:08:07 CDT
I am trying to minimize and equilibrate a protein monomer that consists of
6525 atoms (protein only). I am doing this is vacuum. I receive the
following error in my log file -
REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN
TCL: Running for 2500 steps
ERROR: Constraint failure in RATTLE algorithm for atom 1917!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
This seems to be a common question on the mailing list, so I first read
through some suggestions described previously. I've tried increasing the
cutoff and the pairlistdist. This didn't seem to help. It did change the
atom that seemed to cause the problem, it always seems to be to near the
surface f the protein. I looked at the pdb in VMD and I don't see any
unfavorable overlap between this atom and another. Jim Phillips mentioned
that a good rule of thumb is 1 atom per 10 cubic angstroms. I am working
with a box with periodic boundary conditions. If I have 6525 atoms, I
would need a box that had a volume of 65,250 A^3. The original dimensions
of my box set by the cellBasisVectors are 47,42,44. This would give me a
box with an area of 80,856 A^3. I went ahead and make the box larger by
making all the dimensions 50.
Am I missing something obvious? Any suggestions would be great.
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