Minimization convergence issue

From: Brittany Morgan (
Date: Mon Mar 02 2009 - 09:59:21 CST

Hello all,


I am having a problem with convergence of the minimization routine. The
gradient tolerance convergences rapidly at first, but then fluctuates around
40-100 and will not continue to decrease. If I try to go ahead and run
dynamics, even with a very conservative time step (0.5fs with a 1e-6 SHAKE
tolerance), I get a RATTLE constraint error, but it is not the same atom
every time.


I have tried SHAKE on or off during minimization, varying the length of
minimization from 1,000 to 20,000 steps and I also tried using the velocity
quenching algorithm for 1,000 steps initially and then doing additional
conjugate gradient minimization. Turning SHAKE off during minimization
helped some (fluctuates between 10-40) for one structure at least, but it
didn't solve the problem.


I have never had this problem in the past, and now it is happening for 4
structures. The difference is that I am using psfgen (using a script, not
the GUI) to generate the input files for NAMD instead of using CHARMM. I
can't find any difference when comparing the output of psfgen with the
original PDB files, and the structure after minimization is not very
different from the starting state. I'd prefer not to go back to using
CHARMM, since it is a pain comparatively for me, but I don't know what else
to try.


Any suggestions?



Brittany Morgan

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