Re: [AMBER] Equilibration problem large system in explicit solvent

From: David A Case <>
Date: Wed, 7 Jan 2015 11:29:24 -0500

On Wed, Jan 07, 2015, Waldner, Birgit wrote:
> Has anyone encountered a similar problem and can point me in the right
> direction on how to fix this error? The equilibration of just the
> monomer using the same equilibration protocol works fine.

To add to what Jason said:

It's not clear what the difference between the monomer and the tetramer is.
Using smaller restraint weights is a good idea, but you may want to make sure
that you don't have any bad overlaps in your starting tetramer structure (use
the checkoverlap command in cpptraj); and you may need to carry out
minimization (or more complete minimization) before starting the MD.

...good luck....dac

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Received on Wed Jan 07 2015 - 08:30:02 PST
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