Hi,
As I suggested earlier in this thread, I think the original poster
should run test simulations of a CHARMM36 POPE membrane using either the
NAMD or CHARMM softwares. It has been mentioned a couple of times in the
thread thay there are differences in the implementations of the
switching methods for the van der Waals interactions between softwares,
and in my opinion this is one potential cause of the low area per lipid
for the POPE membrane. This can be tested from these simulations in NAMD
or CHARMM. Another potential explaination is that the relatively short
simulation of Klauda et al. (40 ns) was not converged.
As for other POPE force fields, the standard Berger parameters will not
perform well. There are some force fields that have been reported to
perform well. Apart from a couple of GROMOS ones I know of (GROMOS-CKP
and GROMOS 43A1-S3 - I have used these in the past and both behave well
at 313 K, which is well above the gel-liquid crystal phase transition
temperature of 298 K), all-atom AMBER lipid parameters have been
recently reported that include POPE
(http://pubs.acs.org/doi/abs/10.1021/ct300342n). This may be another
option that could be used for these simulations, with an AMBER force
field used for the protein.
Cheers
Tom
On 15/08/12 20:09, Peter C. Lai wrote:
On 2012-08-15 06:55:59PM +0000, Christopher Neale wrote:
Write the authors of the simulation paper that has a "correct" APL for POPE and
ask them for an input file.
That is really the only way to be sure that you are not doing something
different than they did.
In my experience, people are quite willing to provide you with their input
file(s).
If you still get a different APL than they reported, then see if your
simulation times are similar and repeat your run
a few times to see if it's just statistical noise.
The fundamental problem Sebastian will have is that Klauda obtained their
APLs using CHARMM software, and he is trying to reproduce this using
the forcefield in Gromacs software. So even if the CHARMM input files
were provided, it maybe difficult to exactly reproduce the conditions
in Gromacs (if certain parameters were implemented differently)
Regarding 323 K, I don't recall... it's just a number that sticks in my head.
Perhaps it is for DPPE or DPPC.
I'd still suggest that you at least try POPC. So your peptide binds more
favourably to POPE than to POPC...
that alone does not limit you to POPE. Then again, I don;t know exactly what
you are trying to do.
Chris.
It is generally a good idea to use a higher temp than the phase transition
temperature, since during equilibration close to the phase transition
temp there is a risk of inducing some ordering due to uneven heating.
People run DPPC at 323 because its phase transition temp is 315K. If
POPC's is 271 and people typically run POPC at 300, then it may be wise to
bump up the running temp of a POPE system. Of course, your APL will
inflate at higher temperatures...
-- original message --
My peptide is known to be more favorably to PE than PC membrane that is why I
am using POPE.
Experimentally, the liquid phase transition is at 298K for POPE (if I am not
mistaken). Is your 323K refer to some simulations?
At first I wanted to use the new CHARMM36 lipids parameters because they are
supposed to solve the previous CHARMM27 issue with the area per lipid. However,
I am consistently obtained smaller APL then experiment and I am not able to
reproduce the published APL obtained for POPE, even if I am starting from their
equilibrated 80-POPE membrane and use same simulation conditions. That was the
reason for starting this thread on the mailing list.
Unfortunately, my peptide conformational space in solution is only
well-represented by CHARMM27 (equivalently in CHARMM36), so I can not use
Berger's lipid parameters with OPLS or GROMOS even if it would be preferable as
they do not have APL inconsistency and are united-atom.
I will made some tests in the NPAT ensemble. Perhaps the NPAT effects can be
made neglegible by using bigger membrane compared to my peptide's size (?).
Sebastien
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