Hi,
Yes, I agree with you regarding the combination of Berger and GROMOS
force field and requiring validation. I just wanted to point out the
interactions between the protein and lipid are treated in the same way,
irrespective of the different GROMOS protein force field used (when
using the parameters from lipid.itp).
Further on the topic of validation, the only work I know of that has
studied in detail the Berger/GROMOS combination
(doi:10.1088/0953-8984/18/28/S07) says that when using the standard
method as employed by the parameters in lipid.itp:
"the strength of interactions between hydrocarbon lipid tails and
proteins is significantly overestimated, causing a decrease in the area
per lipid and an increase in lipid ordering"
So the standard approach is probably not the most appropriate way to
combine the Berger lipids and the GROMOS protein force field. Rather
using combination rules (as for example done in the Berger/OPLS
combination) is probably better.
Cheers
Tom
On 19/07/12 00:15, Justin Lemkul wrote:
On 7/18/12 6:57 PM, Thomas Piggot wrote:
Hi,
Justin, I am interested by your comments regarding the CHARMM lipids. In
particular can you elaborate as to why you think that the CHARMM
lipids are
better than the united-atom ones (such as Berger and several GROMOS
variants).
I think there's nothing wrong with Berger lipids, and I myself use
them routinely. They do a decent job of reproducing lipid behavior,
no question. My own use is motivated by historical reasons primarily
since I began work with them many years ago (also around the time that
53A6 was all shiny and new) and I'm trying to keep consistent. It
seems to me that the CHARMM36 parameters are very thoroughly validated
and are very modern. The Berger lipids were developed a long time ago
using very short (by modern comparisons) simulations and old parameter
sets that have since been improved upon. There are numerous
reasonable lipid models out there, to be sure.
As for the original question, the modifications in going from GROMOS
53A6 to
54A7 will not influence the combination with the Berger lipid
parameters, if the
most common approach of using the parameters from the 'lipid.itp'
file is taken.
The interactions between protein and lipid will remain the same, with
the van
der Waals interactions between the protein and lipid treated using
the GROMOS87
parameters as defined in lipid.itp. From my experiences I would strongly
recommend using 54A7 over 53A6, as we have seen instability in short
helices in
53A6 that is not reproduced when simulating the same systems with
several other
force fields.
I agree with this, I'm just a stickler for validation. A test system
using this force field combination should certainly replicate some
known behavior. It's generally accepted that any Gromos derivative is
compatible with the Berger parameters, but I've never seen anyone
demonstrate it systematically aside from their own usage for
particular cases.
For the 'best' force field to choose when simulating a
membrane-protein system,
there is no definitive answer that I (or anyone else) can give you
(yet). My own
opinion is that currently CHARMM36 is probably too slow (given that I
would
strongly recommend the use of the CHARMM TIP3P water model with this
force
field) and that the all-atom protein force fields are probably better
than the
united-atom ones. This means that I would (for a PC membrane) use
Berger for the
lipids with OPLS-AA/L or an AMBER force field for the protein. This
is just my
(current) opinion though, I strongly suggest doing lots of your own
reading
before making your mind up.
Indeed.
-Justin
--
Dr Thomas Piggot
University of Southampton, UK.
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