Generally, forcefields are not parameterized for temperatures other
than 298K, so simulations are not expected to reproduce the expected
properties (like boiling water and the correct temperature
denaturation of proteins).
There's almost certainly other issues here (including the fact that
I'm entirely sure that you can get a lot more than 24 ns of simulation
on a 54 aa protein; and 26 atom of pressure seems pretty arbitrary)
but it will come down to this eventually.
Just because you found a paper in which they get a denatured state
does not imply that they got the correct denatured state.
Chris.
-- original message --
Hi All,
I met a problem when I try to unfold a protein using Gromacs, It
seemed the protein cannot be totally unfolded!
The simulated system has one Engrailed Homeodomain (En) protein (a
three helix bundle protein with 54 residues, 629 atoms), total 4848
spce waters, and 7 Cl- used to neutralize the system in a 5.752(nm)^3
water BOX. I use the NTP ensemble with T=498K and P=26atm. The system
has 1nm thick water in each side of the En protein, and the density of
the system has been adjusted to0.829 g/cm3.
The simulation lasted 24ns. The helixes disappeared at about 4ns. And
after that some beta sheet formed in the N terminal of the protein.
However, the protein kept in a compact state during the 24ns
simulation. The radius of gyration of the protein fluctuated around
1.1nm during the simulation.
I've also noticed similar simulation done by others. For example,
David Becka and Valerie Daggett reviewed their En protein unfolding in
paper "Methods for molecular dynamics simulations of protein
folding/unfolding in solution. Methods 34 (2004) 112¨C120". The
simulations were performed with ENCAD and ilmm, and used an 0.8nm
cutoff range. And the ensemble they used is NVE as I know. A stretched
unfolding state occurred at about 5ns in their 60ns simulation in
498K, with little helix structure.
I was wondering whether the difference is caused by using different MD
software and force field, or by some wrong parameters in my .mdp file.
I've also conducted another 18ns simulation, and the result is almost
the same. I list he mdp file below. Any comment is appreciated!
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
