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
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 pretty clear about how one gets different
factors. I suggest taking a look at the non-peer reviewed .pdf file
that I posted earlier as it contains more details about the method.
If you still have difficulty, perhaps start from the beginning when
writing your question.
If you are simply concerned if the method works as advertised, then
you can search the mailing list to see that I have had this type of
discussion before -- the method works. Also, you can look at the
plot in that .pdf file that shows some evidence that it is working
alright.
Chris.
-- original message --
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 [pairtypes], how about 1,4 electrostatics? Since fudgeQQ is 1, how
is the factor of 2 achieved?
Thanks,
Bin
p.s. your paper looks really good, congrats!
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
