[gmx-users] mass changes in free energy calculations

[David Mobley]

Yes, usually it would be a waste of time and energy to change the mass.

On Fri, Jun 20, 2008 at 10:17 PM, Qiang Li <friendli2000 at gmail.com> wrote:
> 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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