Dear Chris:
Now it makes all sense. Thanks a lot.
And your method surly works great.
Bin
On Mar 15, 2010, at 9:23 AM, chris.ne...@utoronto.ca wrote:
Dear Bin,
I think that you are getting confused here between different
publications. It was the Lindahl, E., and O. Edholm. 2000. paper
tha
Dear Bin,
I think that you are getting confused here between different
publications. It was the Lindahl, E., and O. Edholm. 2000. paper that
you quote below, but recall that they had no protein in that work so
manipulations of fudgeQQ would have been available to them.
The HEDP method is
On Fri, Mar 12, 2010 at 10:06:53PM -0500, chris.ne...@utoronto.ca wrote:
>
> Note that the "Berger" lipids were in fact developed by many people
> and they have come to be named by only one of the contributors. The
> reference that I use for my 1/8 scaling of the LJ 1-4 is:
>
> Lindahl, E., and O
Dear Chris:
Thanks a lot for your reply. That's really helpful. Now I have a
further question:
"1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4
Lennard?Jones interactions a factor of 8."
I can understand that the LJ1-4 can be reduced by simply scale epsilon
in [pairty
Dear Bin:
Read the in-depth procedure here:
http://www.pomeslab.com/files/lipidCombinationRules.pdf
Note that the 0.125 scaling factor is not anything that you need to do
in addition to the files that you can download from Tieleman's site --
it is already included there (you can confirm t
Dear all:
I was trying to convert the lipid.itp downloaded from Tieleman's
website to the format compatible with OPLS. I basically followed the
procedure in this post, which is really helpful:
http://www.mail-archive.com/gmx-users@gromacs.org/msg03459.html
But there is one comment there I d
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