[gmx-users] another pull-code question

chris.neale at utoronto.ca chris.neale at utoronto.ca
Fri Jul 2 15:39:55 CEST 2010

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  

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  


-- 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).


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