I do not know what is the structure of monoolein :((
Then it is strongly possible that OH-C-C-OH is best represented
by the P4 particle type. But it might not be that simple :))
you should once your (first) topology made try it out and compare
to as much data you can find ... experimental and from atomistic
simulations ... that should include dynamics, structure et
thermodynamics ...
have fun,
XAvier.
On Oct 13, 2010, at 2:06 PM, George Khelashvili wrote:
Dear Xavier,
I think I have figured out how to deal with the missing part. My
problem was OH-C-C-OH construct which is the headgroup of monoolein.
After some research, it looks like that it is parameterized based on
ethanediol and has P4 type. The rest of the molecule I guess should
be straightforward CG backbone plus CG tail beads. Can you comment
on this?
Thank you,
George
On 10/13/2010 3:56 PM, XAvier Periole wrote:
Have you considered reading the few papers describing the
principle of parameterization with the Martini FF? There are basic
recipes described and specific applications detailed.
Looking at cgmartini.nl might also help you getting more
information and
reach people involved in Martini parameterization :))
XAvier.
On Oct 13, 2010, at 11:42 AM, George Khelashvili wrote:
Dear users,
I am trying to build Martini topology for monoolein molecule (I
assume that no such topology exists at this moment). It is obvious
that the tail part of the molecule is similar to DOPC lipid tail,
however I am not sure how to parametrize the head-group of
monoolein. I would appreciate if somebody could provide a guidance
on this matter.
Thank you,
George
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
George Khelashvili, Ph.D.
Department of Physiology and Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Room LC501
New York, NY, 10065, USA
gek2...@med.cornell.edu
Phone: 1-212-746-6539
Fax: 1-212-746-6226
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists