[gmx-users] mass changes in free energy calculations

[Qiang Li]

Thanks for clearing the doubt.

Is that more easier to get equlibrium to use unchanged mass when doing LJ
turning on/off?
I ask this since I found the forwards and backwards mutation free energy are
more consistant if I do not change the mass. Accidentally?

LQ

On Thu, Jun 19, 2008 at 4:26 AM, David Mobley <dmobley at gmail.com> wrote:

> 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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