[gmx-users] Some questions about free energy calculation

David L. Bostick dbostick at physics.unc.edu
Wed Jan 9 19:34:27 CET 2002


The parameters all go into the same topology file.. see the section in the
manual on how to write topologies.  This is fed into grompp and in the .mdp
file you specify free_energy=yes and the integrator is md.

Hope this helps,

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Wed, 9 Jan 2002 nicolis at guideo.fr wrote:

> Hello,
> I want to compute the solvation energy for some metal cations. After 
> reading the manual I understand that it is possible to do such a 
> calculation with gromacs using a lamda parameter to generate smoothly 
> a metal in a box of water. Is my interpretation correct? Is this the right way 
> to proceed?
> If yes, I see that I have to define free_energy=yes in the .mdp file but with 
> which integrator?
> And another question: I see that the lamda is used to shift from topology A 
> to B, but where do I feed the two topologies? In grompp ot in mdrun?
> I looked all the manual pages that seemed relevant but I was not able to 
> find the info. If you can point me to the correct place to look, thank you
> Yiannis
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