[gmx-users] another pull-code question

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 2 16:48:07 CEST 2010

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 :)


chris.neale at 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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