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

Berk Hess gmx3 at hotmail.com
Thu Jul 30 10:33:28 CEST 2009


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.


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


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


Express yourself instantly with MSN Messenger! Download today it's FREE!
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090730/7fadd634/attachment.html>

More information about the gromacs.org_gmx-users mailing list