I definitely agree. I think the general point (which I know I've been a bit
off-hand about explaining) is that, if properly applied (key caveat!), just
about any combination of pull method + pull geometry can be used to conduct SMD.
You're quite right that just trying to shoot some molecule across your system
can have terrible effects for complicated environments. What I've always meant
is that people shouldn't feel constrained to using only the settings I have in
the tutorial, since they are not the most versatile.
I think I'll add some discussion on this topic to my tutorial, which seems to
have become quite popular. I guess I was hoping that people who used the
tutorial would refer to my paper (from which the tutorial is derived), wherein
we demonstrate that our results were not influenced by the pull rate (with both
k/2 and k/10). Maybe I should make such things more obvious :)
-Justin
chris.ne...@utoronto.ca wrote:
Hi guys,
I just wanted to chime in on the idea that "how you perform the initial
pulling to get structures isn't all that important" because I strongly
disagree and think that it is, in general, immensely important.
OK, it's actually not important if we're talking about pulling two Na+
ions, or two entirely rigid molecules in water, because you are not
going to affect their conformations by pulling too quickly. However,
let's take the other extreme and say that one wants to generate initial
conformations of something in a bilayer or an ion in a membrane channel.
In these cases, initial pulling that is too fast can push the bilayer,
ligand, or protein so far out of its equilibrium conformation that your
US will not sample enough simulation time to re-equilibrate.
To sum-up my point of view, the initial pulling simulations should be
done as slowly as you can afford, and if you want to have some
confidence that your rate is "slow enough", then you should probably run
at rate=k and rate=k/10 and check that the starting structures that you
get are not separated from each other by huge barriers resulting from
some non-equilibrium response at rate=k that was not observed at
rate=k/10. Even if you don't go through some procedure like the one
above, there is still no need to take risks by limiting your setup
pulling simulation to 1 hour of simulation when you're going to then
spend the next 2 months doing US (garbage in = garbage out).
Chris.
-- original message --
For umbrella sampling you need to steps:
1) get the configurations for the later umbrella sampling (step 5 in
Justins tutorial). How you perform the pulling sim. for that isn't
important, you only need the structures.
2) umbrella sampling (step 6 in tutorial). Here you use the
configurations from step 1. I think here you can only use
"pull=distance" (i think).
Greetings
Thomas
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
