[gmx-users] Martini parameters for monoolein
x.periole at rug.nl
Thu Oct 14 01:30:02 CEST 2010
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
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,
> 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 :))
>> 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,
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> 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
> gek2009 at med.cornell.edu
> Phone: 1-212-746-6539
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