Re: [AMBER] All Energy Calculations in AMBER18.

From: Daniel Roe <>
Date: Fri, 28 Dec 2018 09:21:01 -0500


On Tue, Dec 25, 2018 at 8:54 AM DHEERAJ CHITARA <> wrote:
> Dear AMBER Users,
> How to perform energy calculation using cpptraj in AMBER 18.

Depends on what kind of energy you're after. The 'energy' command when
given with little to no keywords will default to calculating bond,
angle, dihedral, 1-4 interaction, and nonbonded energy using a very
simple model (basic Coulomb and LJ 6-12) with no cutoffs. If your
coordinates have unit cell information you can use more advanced
models for nonbonded interactions, including PME (assuming PME support
was compiled in which requires C++11 and FFTW). Alternatively you can
use the 'esander' command to calculate energy via the libsander
interface (also assuming support for this was compiled in) - the
advantage of 'esander' is that it has GB methods available. See the
Amber 18 manual (section 30.10.28) for full details.

> I used the following command
> *"energy LOX_Aq out LOX_Aq.dat" *without striping water and it will take
> too much time to execute.

The 'energy' command is OpenMP-parallelized, so use cpptraj.OMP if
that is available. Cpptraj does not benefit from hyperthreading, so be
sure that OMP_NUM_THREADS is set to only the available number of
physical cores if your CPU has HT turned on.


> Should I strip out ions, water and crowder in this calculation.
> --
> ----
> Dheeraj Chitara
> _______________________________________________
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Received on Fri Dec 28 2018 - 06:30:03 PST
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