Thanks, Dave!
I actually meant to say all the other electrostatic energies besides the 1-4 ELEC. The atom pairs that are more than 3 bonds away are counted and the electrostatic energies are summed up. Is this correct as well?
Best,
Lin
> On Sep 3, 2019, at 5:08 PM, David Cerutti <dscerutti.gmail.com> wrote:
>
> That's how it is calculated. The sander and pmemd programs read a list of
> 1-4 interactions from the topology file, compute the scaled ELEC and VDW
> terms, and make running sums of those energies. The mdgx program looks at
> the topology and decides for itself which atoms are separated by exactly
> three bonds, no more, no less. The results should be identical--the only
> case where I've seen them differ are cases where the non-tleap topology had
> it wrong (double-counting some 1-4s), which sander and pmemd did not check.
>
> Dave
>
>
> On Tue, Sep 3, 2019 at 3:09 PM Song, Lin <songlin3.chemistry.msu.edu> wrote:
>
>> 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.
>> &cntrl
>>
>> imin=1,maxcyc=0,igb=0,
>>
>> ntb=0, cut=9999,
>>
>> /
>>
>>
>> Best,
>> Lin
>>
>>
>>
>>
>>> On Aug 30, 2019, at 12:59 PM, David Cerutti <dscerutti.gmail.com> 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 <songlin3.chemistry.msu.edu>
>>> 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 - 14:30:03 PDT
