Hi Justin,
I wonder if you could expand upon the following statement, or perhaps
offer some links or references.
"Some argument can be made that N-H is more applicable to membrane
simulations."
I am interested because I use a Berendsen thermostat for membrane
simulations. To be entirely honest, I have no particular understanding
of the consequence of this choice beyond the oft-heard statement that
Berendsen T-coupling doesn't yield the correct ensemble. But it is
very intuitive and, as you say, it's usage is quite common and I have
thus far relied on these points to guide my choice of
temperature-coupling algorithm. Therefore I am hoping to take
advantage of this opportunity to learn a bit more about temperature
coupling as you seem to understand it quite well.
I am hoping that you can outline the logic underlying the 'correct
ensemble' statement and indicate how this is especially applicable to
membrane simulations.
I do realize that this is a large request on this type of mailing
list. Please feel free to decline.
Much obliged,
Chris.
-- original message --
I have used the Berendsen method almost exclusively in my simulations,
and it is
widely used in most of the literature I read. While the argument can be made
that Nose-Hoover gives a result closer to the true ensemble than Berendsen, I
think both are sufficient for simple protein in water simulations. Some
argument can be made that N-H is more applicable to membrane simulations.
As for whether or not you need to slowly increase the temperature, it
is really
up to you. Usually such rigor is not necessary, as often position restraints
are applied to the protein during initial equilibration. I have never
experienced any adverse effects of simply setting the initial temperature,
although that's not to say it's not possible :)
Just my $0.02.
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
