Re: [AMBER] Print non bonded pair list

From: Song, Lin <>
Date: Tue, 3 Sep 2019 19:09:06 +0000

Hi Dave,

Thanks for the info! I have one more question related to this. Is the ELEC energy (generated by AMBER using the following input file) calculated by the this way: first, count all the atom pairs that are 3 bonds away from each other; second, calculate each pair’s electrostatic interaction and sum them up?

AMBER input file.
  ntb=0, cut=9999,


> On Aug 30, 2019, at 12:59 PM, David Cerutti <> wrote:
> 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)"
> energies.
> Dave
> On Fri, Aug 30, 2019 at 12:40 PM Song, Lin <>
> wrote:
>> 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
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Received on Tue Sep 03 2019 - 12:30:02 PDT
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