[gmx-users] oplsaa force field

[Justin Lemkul]

On 12/16/12 11:55 PM, Shine A wrote:
> Sir,
>
>       I studying the dynamics of membrane proteins.First I did a 20 ns
> simulation using GROMOS96 53a6.This force field cause some problems in the
> helical part of the protein.Now I am trying to do the same simulation with
> opls-aa force field.Is the changes I should have to do in ffnonbonded.itp
> and ffbonded,itp is same as in the justin manual?
>

The concept is the same, but the actual information will be very different.  As 
I recall, there are OPLS-AA lipid parameters somewhere out there, but I've never 
used them personally.  One can also implement a hybrid approach wherein the 
Berger lipids can be made compatible with OPLS-AA.  There's a link to that 
method in my tutorial and it has been discussed on the mailing list at length.

For what it's worth, the helical instability is almost certainly due to the use 
of 53A6, which is known to over-stabilize extended configurations and 
under-stabilize helices.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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