[gmx-users] Some questions about free energy calculation

[David L. Bostick]

Hello,

I have never done anything like that before, but if I were to try, I would
first equilibrate a box of water, then place the ion wherever I saw fit
into the resulting configuration.  I would then add the ion into the
topology.  If the only parameters which involve interaction of Zinc with
its environment are for LJ interaction and charge, then use slow growth to
change the charge from 0 to +2 and the LJ constants from 0 to their desired
values by specifying them as topologies A and B.  If the Zinc is in the box
but doesn't interact with solvent until lambda is increased by its first
step, DELTA(lambda), there is no need to do anything with dummy atoms... at
least in principle, I guess.

Not only should you do the reaction along the lambda-path in forward and
reverse, but you should use the hysteresis in order to get an estimate of
the precision... Slow growth can be tricky statistically speaking...  for
more, see the literature on "Thermodynamic Integration" (TI).

I hope this helps,
David

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
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 Thu, 10 Jan 2002, Yiannis Nicolis wrote:

> At 13:34 -0500 9/01/02, David L. Bostick wrote:
> >Hello,
> >
> >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,
> Yiannis
> 
> >David
> >
> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >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
> >>
> >>  _______________________________________________
> >>  gmx-users mailing list
> >>  gmx-users at gromacs.org
> >>  http://www.gromacs.org/mailman/listinfo/gmx-users
> >>  Please don't post (un)subscribe requests to the list. Use the
> >>  www interface or send it to gmx-users-request at gromacs.org.
> >>
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
>