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!
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 this for
yourself by looking at the topologies downloaded form there). This
is because the 0.125 scaling (1/8 scaling) of 1-4 LJ is part of the
original Berger lipids.
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. Edholm. 2000. Mesoscopic undulations and
thickness fluctuations in lipid bilayers from molecular dynamics
simulations. Biophys. J. 79:426?433.
where they state in the methods:
"1,4 electrostatic inter-actions were reduced a factor of 2 and 1,4
Lennard?Jones interactions a factor of 8."
I believe that this idea originated in a Jorgensen paper looking at
bulk simulations of n-alkanes, but ashamedly I can't recall for sure
at this moment. If you need it, I can look it up next week (let me
know).
BTW, the half-epsilon double-pairlist method is finally published.
The reference is Biophys J. 2010 Mar 3;98(5):784-792. "An Iris-Like
Mechanism of Pore Dilation in the CorA Magnesium Transport System."
Chakrabarti N, Neale C, Payandeh J, Pai EF, Pomès R.
In our paper, I attempt to give a more complete description of the
development of this lipid forcefield by writing:
The parameters for DMPC lipids (10) were the united atom
representation first proposed by Egberts et al. (18), with charges
from Chiu et al. (19) adjusted by Berger et al. (20), and with the
additional scaling of 1-4 coulombic terms introduced by Lindahl and
Edholm (21).
My description of the HEDP method in the referenced paper is thus:
We mixed the OPLS-AA protein force field with the Berger lipid
parameters consistently by applying the half-epsilon double-pairlist
method introduced in this work. This method avoids
reparameterization (22) and retains the original parameters with
greater fidelity. Specifically, the epsilon-values of the 1-4
Lennard-Jones (LJ) parameters of the lipids are divided by two in
the pair types section of the GROMACS input file, and the list of
1-4 interactions is duplicated in the topology file of each lipid.
The regular OPLS combination rules are then applied. In this way,
the lipidic LJ and Coulombic 1-4 parameters are both cut in half and
then included twice to yield properly scaled 1-4 interactions for
both lipids and OPLS protein.
Hope this helps,
please post again to the list if you have further question.
Chris.
-- original message --
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 don't understand:
after changing c6/c12
to sigma/epsilon. (gives effective fudgeLJ of 0.125).
Can someone please explain what this means? Why do I have this
effective fudgeLJ?
Thanks a lot,Bin
--
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
