Re: [AMBER] Troubleshooting SHAKE problems in minimization

From: David A Case <>
Date: Sun, 27 May 2018 09:06:47 -0400

On Sun, May 27, 2018, Alen Ahmetovic wrote:

> As the title suggests I'm running into problems with getting complexes
> through minimization. Below is the minimization input I am using:
> I tried to use cpptraj but since
> minimization restricts the complex, there is no trajectory file to input to
> view to check for atom overlaps, etc.

I'm not sure exactly what this means, but you can and should use cpptraj
to check for overlaps in your starting structure. (Set trajin to whatever
coordiantes you are using to start the minimization.) Also, set ntpr=1 to
get more information about the progress of energy.

Finally, I'm seen cases where it is helpful to set ntmin=2 (only use
steepest descent minimization.) This is slower but can occasionally be
more stable. (This essentially turns off the change of behavior after
ncyc steps.)

...good luck....dac

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Received on Sun May 27 2018 - 06:30:04 PDT
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