[gmx-users] generate pair list and 1-4 interactions

Enemark Soeren chees at nus.edu.sg
Thu Jul 30 11:07:49 CEST 2009

Hi Berk,

Thanks for your answer, I am happy to have the priority list for how the
van der Waals term of the pair potential is calculated.

About fudgeQQ, do you mean that the pair potentials' coulomb terms are
scaled with the fudgeQQ value, even when "gen-pairs" is set to "no"?


( I see from the manual that "FudgeLJ is only used when generate pairs
is set to 'yes', so maybe your answer is already given in the manual.
Actually, I am not sure if this statement is an implicit information
about FudgeQQ..)





From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Berk Hess
Sent: Thursday, July 30, 2009 4:33 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] generate pair list and 1-4 interactions



The charges are always scaled with fudgeQQ.

For the LJ parameters the precendence is:

For an atom pair in the [ pairs ] section with type A and B:
if parameters are present on the line in the [ pairs ] section use
those, otherwise
if parameters are present in the [ pairtypes ] section use those,
if gen-pairs=no generate a fatal error, otherwise
if parameters for A-B are present in the [ nonbond_params ] section
scale with fudgeLJ and use those, otherwise
use the parameters for A and B in the [ atoms ] section and scale with
fudgeLJ and use those.



Date: Thu, 30 Jul 2009 15:58:40 +0800
From: chees at nus.edu.sg
To: gmx-users at gromacs.org
Subject: [gmx-users] generate pair list and 1-4 interactions 

Dear all,

I am a bit confused about how the pair potentials (PPs)are calculated.


If I state explicitly sigma and epsilon values for the pair potentials,
can I then still have a coulomb scaling of my 1-4 interactions?

Say I set "gen-pairs" to "yes", although I have all possible pair
potential interactions specified under "[ pairtypes ]", would I then
still be able to scale my 1-4 coulomb interactions by setting a
"FudgeQQ" different from 1? Also, would I be able to scale the already
given van der Waals interactions with "FudgeLJ"?


Finally, are generated pair potentials based on the parameters specified
under "[ atomtypes ]" or "[ nonbond_params ]" (if the latter exist) in
the ffamber03nb.itp file?


Best regards,

Soren Enemark




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