Re: [AMBER] Print non bonded pair list

From: David Cerutti <>
Date: Fri, 30 Aug 2019 12:59:34 -0400

The point of a pair list is to cull the total number of non-bonded
interactions based on the arrangement of the system in space at a given
time, so there would be no way for ParmEd to do it. To print them with
pmemd, you'd need to go into the inner loop and shout every time it did a
pair. In pmemd.cuda, you'd need to allocate a big array and write to it,
incrementing a counter atomically, every time any thread performed an
interaction in kNLCPNE.h (and there are three places in that file where it
might perform such an interaction). Then you'd need to download the array
from the device and print it with the CPU. The program does not store an
enumerated list of non-bonded interactions, but rather a list of particle
groups that are likely to interact with one another. The non-bonded VDW
and ELEC energies, however, are already output is the mdout, partitioned
into 1-4 non-bonded and "all other (including Ewald reciprocal space sum)"


On Fri, Aug 30, 2019 at 12:40 PM Song, Lin <>

> Hi all,
> May I ask if there’s a way to print all the non bonded pair list and
> corresponding VDW and ELEC energies? Given the prmtop and inpcrd file. I
> know Parmed can print out all the bond, angle and dihedral info, but not
> sure about the non bonded pairs.
> Thanks!
> Best,
> Lin
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Fri Aug 30 2019 - 10:30:01 PDT
Custom Search