Hey Chris,

 

It is actually not necessary to go to the code. You can do that by compiling a 
version of gromacs including the plumed path for free energy calculations. 
Amogst the several collective variables included there there is gyration radius.

 

Regards

 

Felipe
----Mensaje original----De: chris.neale@utoronto.caFecha: 29-mar-2012 
10:50Para: <gmx-users@gromacs.org>Asunto: [gmx-users] Umbrella sampling along 
Radius of gyrationIt is not clear to me how one would do this with MD. The only 
thing  that I can think of doing in gromacs is to create a virtual particle  
that is placed at the center of the protein and then apply forces  along the 
vector from this virtual atom to each of the Ca atoms. You  would need to 
modify the gromacs source code so that the Rg was  calculated at each step and 
the magnitude of each force is scaled  appropriately such that you get a 
harmonic potential about the desired  value of Rg. It should be easier to do 
with MC (although that's a ways  off for gromacs unless I've missed 
something).Some people appear to have done exactly what you want with MD. I  
presume that they used charmm.http://www.pnas.org/content/94/19/10161.long (and 
their reference 22).Chris.-- original message --Hi,   Is there any way in 
gromacs to use radius of gyration of a polymer  as reaction coordinate for 
umbrella sampling ?ThanksSanku-- gmx-users mailing list    
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