nonequilibrium SMD with fixed atoms

From: Ekaterina Sobakinskaja (Ekaterina.Sobakinskaja_at_jku.at)
Date: Wed Jan 24 2018 - 09:27:28 CST

Dear NAMD users,

in my simulations I need to rotate 2 helices in the protein complex to
obtain conformation I need. Other helices must remain in their places.

I'm going to use nonequlibrium SMD protocol. I was trying the example
GlPt, given in the Tutorial, and fixed few helices in the protein, using

fixedAtoms          on
fixedAtomsFile      fixed_atoms.ref
fixedAtomsCol       B

I have also modified colvars.conf accordingly.

The simulations were started, but then I got the error message:

Reason: FATAL ERROR: Error in the collective variables module: exiting.
colvars: Too many iterations in routine jacobi.
FATAL ERROR: Error in the collective variables module: exiting.

How can I resolve it? Or may be I should use another method to solve my
problem?

Any help will be appreciated!

thank you in advance,

Katja

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