Re: [AMBER] AMBER 14 DPFP single energy calculations inconsistent

From: Ross Walker <>
Date: Fri, 30 Jan 2015 12:03:36 -0800

> ​This was something I fixed a while ago. I will preface this with the
> statement that 1.7 angstroms is the correct value. C1, C2, and C3 were, in
> the early days of the Amber force field, reserved for UA force fields where
> the number indicated how many hydrogens were folded into that carbon. So
> the C1/C2/C3 atom types were assumed to have a larger radius (2.2 A) with a
> larger mass (13.02 amu). Unfortunately, Amber has a hard-coded limit of 2
> characters per atom type, and the C1, C2, and C3 atom types were hijacked
> for use in the AA force fields (as there haven't been any UA Amber force
> fields developed in some time), but the LEaP code was never updated for
> this.​ I fixed this in November, 2013, so the first version of leap to
> have this fix was Amber 14.
> ​Long story short -- don't use leap 12 :). Scott -- is the 2.2 A the root
> cause of the issue?

The issue is how 2.2A could cause a problem - since it should be valid. Unless it leads to some overflow in the GPU code somewhere which is possible. The key test will be with the patched code does DPFP with the 2.2A radii give the same answer as the CPU code (PMEMD and Sander) with the 2.2A radii.

All the best

|\oss Walker

| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
| | |
| Tel: +1 858 822 0854 | EMail:- |

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Received on Fri Jan 30 2015 - 12:30:05 PST
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