[gmx-users] Some questions about free energy calculation
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
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?
>David Bostick Office: 262 Venable Hall
>Dept. of Physics and Astronomy Phone: (919)962-0165
>Program in Molecular and Cellular Biophysics
>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:
>> 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
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