Re: [AMBER] inquiry regarding minimum-image convention in cpptraj

From: Daniel Roe <>
Date: Mon, 24 Feb 2020 09:39:51 -0500


On Sun, Feb 23, 2020 at 2:13 PM Akshay Prabhakant
<> wrote:
> We ran the MD using PBC, but
> it seems that while running LIE(the tool from CPPTRAJ), it does not seem to
> have used the PBC while calculating the VDW/EELEC energies .

What made you draw this conclusion? More details would help us
diagnose any potential issues.

>Does the
> cpptraj tool in AMBER use the minimum-image convention(i.e. the periodic
> boundary conditions)? If yes, should any arguments be specified/ command
> needed to be run? If no, then how can we generate potential energy between
> 2 masks using PBC, for a given .nc trajectory file?

The 'lie' action does indeed use the minimum image convention for
distances. From the Amber19 manual (30.11.4 lie):

"The electrostatic interactions are calculated according to a simple
shifting function shown below. The data file
will contain two data sets—one for electrostatic interactions and one
for van der Waals interactions. Periodic
topologies and trajectories are required (i.e., explicit solvent is
necessary). The minimum image convention is

Hope this helps,


> Thanking in advance,
> Akshay.
> _______________________________________________
> AMBER mailing list

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Received on Mon Feb 24 2020 - 07:00:02 PST
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