[gmx-users] mass changes in free energy calculations

[David Mobley]

You can change the mass if you like. Basically, the net free energy
change associated with changing the mass should end up being zero so
it will be irrelevant. The mass of course affects the dynamics and
things like the velocities, but based on equipartition you can
convince yourself that the free energy change will be zero.

David

On Fri, Jun 13, 2008 at 12:04 AM, friendli <friendli2000 at gmail.com> wrote:
> Dear all,
>
> I am calculating FE using TI. I have a question about mutating existing
> atoms with different mass.
> for example, using ffG53a6 force field, in one case i need to mutate CH2 to
> CH3,
> should I use
> [ atoms ]
> 17        CH3      2    ALA     CB      6          0     15.035     CH2    0
>    14.027; qtot 1
>
> OR
>
> 17        CH3      2    ALA     CB      6          0     15.035     CH2    0
>    15.035; qtot 1
>
> I notice from Prof. Alan Mark's online FE course, he mutates a H atom to a O
> atom, but does not change its mass.
> The line is :
> 12    HC        1     PHE       HZ          6           0.1        1.008
>   OA         -0.548        1        1.008
>
> Can somebody explain a bit why we should not change the mass accordingly?
>
>
> thank you
>
> LQ
>
> I though I sent this email but why I can not see it. There may be something
> wrong with my email software. so I send here again. sorry
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