Re: [AMBER] Using polarized force field lead to large RMS in the second step of minimization

From: Jason Swails <>
Date: Fri, 22 Aug 2014 12:10:56 -0400

On Fri, 2014-08-22 at 22:56 +0800, 张冬冬 wrote:
> Hi,
> Thanks very much for your suggestions last time. Now that problem has
> been solved. Many thanks.
> At present, I have a new question emerging on my test of running
> minimization using a restraint file. The restraint file is regarded to
> four distance restraints between some atoms. After every minimization,
> I observed the results in the VMD, checking the four distances defined
> in the restraint file. In the step three of minimization, the four
> distances group in the restraint file, however, turned to be above the
> defined upper distance, which should not happen in this situation. On
> the other hand, in the MD step, by observing another test, I find
> that the distances group in the restraint file are strongly met with
> distance range, neither below the lower distance nor above the upper
> distance. So, I wonder that, whether the restraint file is not
> effective in the minimization. Thank you!

The restraint file should be read in for minimization, and it will
modify the potential... if you've done it correctly.

You can tell quickly whether the restraint potential has been applied or
not by looking at the mdout file. There is a RESTRAINT component of the
energy that should be equal to the penalty imposed by the restraint
potential. If it is zero for every step, then your restraint potential
was not applied and you have to figure out what is missing in your input
file. If it is non-zero, then your restraints are likely not strong
enough if they are being violated too much.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Aug 22 2014 - 09:30:02 PDT
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