FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Jones de Andrade
johannesrs at gmail.com
Tue Feb 13 06:52:18 CET 2007
Well, I'm not "exactly" trying t reopen an old discussion. I'm trying to see
a different aspect from it, as the subject indicates.
Since the message reproduced below is the last of the "fudges" questions,
I'm worried about the fact of the fudgeLJ meaning nothing for the
First, is it true, and there is no way around to get a working fudge LJ of
0.5 AND a fudgeQQ of 0.8333 in gromacs simulations?
Having this in mind, shouldn't it mean that the ffamber, the amber port to
gromacs, have a "problem" in that point? Specially because it uses, up to
the point I could see, the same "configurations" in the "default" section?
I have deep concerns on this because I would like to move on to gromacs to
make the next simulations I'm interested in. My interests in gromacs range
from its speed to simplicity and range of analysis programs it already have
(and, of course, the cost of the program). But this specific point is a big
reason of concern to me, and I would like to see it clarified.
Thanks a lot for any help in advance.
On 12/7/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> > I am puzzled about this. In your opinion, when I use genpairs=no,
> > 0.5 and fudgeQQ=0.8333, are these scaling factors, 0.5 and 0.8333,
> > On the other hand, when using genpairs=yes, how to set the scaling
> factor of
> > fudgeLJ and fudgeQQ?$
> fudgeQQ is always used no matter what the value of genparis is.
> (exerpt from
> Each force-field has its own rules (e.g. gen-pairs and FudgeLJ/QQ), but
> apply to the information outlined above. For example, gen-pairs does NOT
> "generate a [ pairs ] section for the molecule." Instead, it means "If
> epsilon and sigma are not present in a [ pairs ] section entry, and
> that type of
> interaction is not explicitly formulated in [ pairtypes ], then it is
> permissible to use the regular non-bonded parameters, and in that case
> them by FudgeLJ."
> Therefore your settings indicate that coulombic 1-4 interactions will
> be scaled by 0.8333 and the pairs must be taken directly from the [
> pairs ] or [ pairtypes ] section (and they will NOT be scaled by
> fudgeLJ). In your case fudgeLJ does not matter (you could change the
> value and it would not affect your simulation). However, I have always
> hoped that it is set to 0.5 to indicate that this is what the
> forcefield developers have done for you and included it in [ pairtypes
> ] so that it's kind of a reference value for your piece of mind.
> I was assuming that the previous messages were from an Amber
> forcefield. Since Amber uses (to my knowledge) [ pairtypes ] instead
> of genpairs=yes, I was confused by the combination of genpairs=yes and
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