Re: [AMBER] Errors in AmberTools14

From: Jason Swails <>
Date: Fri, 13 Mar 2015 16:32:13 -0400

On Fri, 2015-03-13 at 15:28 -0400, Jonathan Gough wrote:
> I believe that something IS off when the output is parsed by sander. Our
> calculations (on the energy) are WAY off. That's how I came across the
> errors. The data from one node was correct and the output of the other was
> off.

How are you using ParmEd? The diffs you showed only look like small
round-off values. And they're not even in the charge section as I
originally thought -- they're in the Lennard-Jones A- and B-coefficient
sections. Since these involve raising a value to the 6th and 12th
powers, you lose precision pretty quickly with them. So round-off is
not entirely surprising.

Can you point me to a particular number that is wildly different between
the two versions? Because I'm not seeing one.

Once I know more details of your workflow, I'll hopefully have a better
idea of where to look for the problem.

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Mar 13 2015 - 14:00:02 PDT
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