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

From: Waldner, Birgit <>
Date: Thu, 8 Jan 2015 08:30:30 +0000

Thank you very much, both of your replies were very helpful. The tetramer starting structure was without any bad overlaps or clashes. It indeed was a problem of the exaggerated force constant. After reducing the force constant by a factor of 100, the whole equilibration process proceeded without any further problems.

Best regards,

From: David A Case []
Sent: Wednesday, January 07, 2015 5:29 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Equilibration problem large system in explicit solvent

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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