[gmx-users] Some questions about free energy calculation

Yiannis Nicolis nicolis at guideo.fr
Thu Jan 10 22:54:28 CET 2002

At 13:34 -0500 9/01/02, David L. Bostick wrote:
>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,

Yes it helps thank you. I had looked at sections 3.12 and 4.3 but I 
missed 5.6.4
Another question: if I want to grow a ZN2+ from nothing (or the 
reverse way) is it sufficient to give  a 0 mass and 0 charge, or I 
have to go to a dummy atom (in other words, I see how to change the 
atom type but how do I make an atom appear or dissapear?)
Or is it better to change the zinc in water instead of making it vanish?
Thanks again,

>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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