Just to make sure we all agree on the physics behind lipids bilayer
simulations. For a 2-D free standing bilayer, the proper and ONLY
correct value of surface tension is EXACTLY equal to ZERO. TO be
precise, I refer to the external surface_tension parameter one adds to
the simulation. The system per se of course has its own surface tension
that is not zero.
Anything different than surften=0 requires some explanation as to why it
is needed.
The basic explanation is that unless you put a value there, the
simulation does not reproduce neither order parameters nor area per
lipid. The reason is most likely one of the force field, as is, not
being able to work without the correction.
Since Charmm and now Amber have not really been able to figure out a
lipid force field that DOES NOT require an extra surften, it is possible
that there is a problem with fixed charges force fields, but I have no
proof of that.
In any case, the proper value of surf_tension, for a given simulation,
is the one that reproduces experimental data for structural properties.
The value CANNOT be guessed from experimental literature values of
surface tension, it must be calibrated for the force field. Hence, Ross'
plot is the goto value so far.
Adrian
On 6/15/12 6:28 AM, Albert wrote:
> On 06/15/2012 12:02 PM, Ross Walker wrote:
>>> Moreover, the surface tension values probably should also have
>>>> something
>>>> to do with the cutoff we use..... I don't know whether Ross have any
>>>> comments on this aspects.
>> No it should NOT depend on the cutoff. Why would you think it should depend
>> on the cutoff?
>>
>> If it does then your cutoff is TOO SMALL, period!
>>
>> I suggest you check things carefully. Ultimately if you want to publish the
>> work you will need to defend the surface tension you used so you might as
>> well run a few hundred nanoseconds for the system you want to run with a
>> range of surface tension values and then you'll be able to provide a
>> justification of the value you used if a reviewer asks.
>
> that's strange, because in recent CAHRMM workshop, the speaker emphasize
> this issue and they state that the non-bonded cut off should influence
> the surface tension.....
>
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--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Fri Jun 15 2012 - 07:00:04 PDT
