[gmx-users] Pull code using two reaction coordinates??

XAvier Periole x.periole at rug.nl
Mon Mar 16 23:34:49 CET 2009

Hi Rodney,

the other alternative is to define the springs in your topology file.  
You first need to merge
your groups (is part of different molecules) and run the different  
combination you need by
defining them by hand; you can easily write a awk script to generate  
the different topologies
you need.
Then you can use a 2D wham to combine the different histograms you've  
obtained and
get your 2D PMF.


On Mar 16, 2009, at 8:28 PM, <rversace at ccny.cuny.edu> <rversace at ccny.cuny.edu 
 > wrote:

> Hello everybody:
> I am trying to perform some PMF calculations using the pull code  
> with a spring (umbrella sampling) but using two reaction coordinates  
> (E1 and E2) between four different groups (r1,r2,r3 and r4).
> All the examples and tutorials that I found so far on the web, only  
> mention PMF calculations for one reaction coordinate (E1) between  
> two different groups (r1 and r2).
> Is it possible to perform the calculations using two reaction  
> coordinates at the same time or should i do two different individual  
> calculations or there is something more that i should do to achieve  
> it?
> I will appreciate any help.
> -Rodney
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