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

Chris Neale chris.neale at utoronto.ca
Mon Mar 16 23:06:59 CET 2009

Hi Rodney,

This may be possible if your reference is absolute coordinates. In this case, just use pull group 1 and 2, with the 
reference group undefined. For more nuanced usage, the problem is that you are only allowed one 
reference group (and one type of pull code usage) in a given run. 

I put a request for this type of functionality on the wiki wish list a long time ago and it never materialized, so my best
guess is that it will not be done in the near future.

Quoting http://wiki.gromacs.org/index.php/Development:
"* The ability to read in multiple .ppa files, for example to allow one pull-code implementation of an umbrella in 
absolute coordinates and one relative to a reference group, or one umbrella and one constraint and one afm, etc.
* Since the pull code is now integrated into the mdp file in gromacs 4, this request now has a different format, 
but the functionality requested remains the same."

You might be able to do something with special "bonds" if you can't use an absolute reference.


-- original message --

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.

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