A few notes:
- the original method (Kumar-JCC-1992) that inspired wham was actually
developed to mix different temperature simulations. It is however not
clear
for the type of system you are simulating how much a 500K simulation
would be useful to improve the sampling at 300 K or so. The reason is
that the enthalpy difference between the two systems is so high that the
probability that a conformation from a 500K simulation would contribute
to sampling at 300K is really low. It would much more efficient for
systems
with implicit solvent for which the energy of the system does not vary
so
much with the temperature. One could look at Chodera-JCTC-2007
and ref therein for a few examples.
- I would think that a REMD simulation would be more useful. No need to
run 30 replicas to very hight temperature! A bilayer at 500K might get
funny.
- Martini force field for flexible regions of protein should not be
trusted ... or
really interpreted with a lot of reserve. The "coil" definition is
simply something
flexible with absolutely no guaranty that it could be representing
some thing
even close to reality, which we have only an approximate idea of what
it is!
- A peptide in a bilayer has a very high chance to get into a helical
conformation.
Do you think it is reasonable to keep it "flexible"?
- As noted by Justin and Chris, you definitely have a problem of
convergence ...
I am not sure how many "converged" examples of PMFs of peptide
crossing a
bilayer are out in the literature (Justin?) but from our experience
with Martini
it does take an awful lot of time to really get convergence. For you
system I
would expect at least a microsecond for the windows where sampling is an
issue. As an example, we saw significant differences on a PMF between
two
simple helices up to 8 us ... and no charges were involved.
This might be a lot pessimistic but you should not get fooled by a CG
model.
Martini is really good for a lot of things but other things should
really but be
looked at carefully.
XAvier.
On Feb 22, 2011, at 9:12 AM, Jianguo Li wrote:
Sorry I forgot to attach my mdp files.
Here is the mdp file for pulling simulaition:
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