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

[Berk Hess]

Hi,

FudgeQQ is always used, independently of gen-pairs.
I have added a note about this in the manual.

Berk

Subject: RE: [gmx-users] generate pair list and 1-4 interactions
Date: Thu, 30 Jul 2009 17:07:49 +0800
From: chees at nus.edu.sg
To: gmx-users at gromacs.org



















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..)

 

-Soren

 

 





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





 

Hi,



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, otherwise

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.



Berk







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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