On 4/1/20 8:57 AM, Andrey Gurtovenko wrote:
Dear Justin,
thank you for the clarification.
I think my confusion is in part due to the urea topology file
used in the manual as an example, which does not contain
the [pairs] section.
Urea is probably a poor example because it actually doesn't have 1-4
interactions since the H atoms have no LJ. So any [pairs] that are
defined will have all zero parameters.
-Justin
with kind regards,
Andrey
On Wed, Apr 1, 2020 at 3:32 AM Justin Lemkul <jalem...@vt.edu> wrote:
On 3/31/20 12:59 PM, Andrey Gurtovenko wrote:
Dear All,
Recently I realized that I don't fully understand what should be done
in Gromacs to account for 1-4 LJ interactions.
According to the manual:
"gen-pairs is for pair generation. The default is ‘no’, i.e. get 1-4
parameters from the pairtypes list. When parameters are not present in
the list, stop with a fatal error. Setting ‘yes’ generates 1-4
parameters that are not present in the pair list from normal
Lennard-Jones parameters using fudgeLJ."
http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html
Therefore, I had an impression that to account for 1-4 interactions in
some generic force-field, it is enough to
set gen-pairs=yes.
However, it turns out that this is not the case:
in addition to gen-pairs=yes, one has to EXPLICITLY list pairs in the
[pairs] section of the topology file of a system.
Otherwise 1-4 interactions are NOT accounted for.
Can someone comment on this?
If I am right, maybe it is worth to clarify this point in the manual?
The language in the manual is correct, either pair *parameters* are
generated, or they are not. The topology is different from the
parameters; if *interactions* are not there, then nothing is done.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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