[gmx-users] Clarity on TI free energy terms

[Nash, Anthony]

Hi Hannes,


Many thanks for the reply. With regards to your final comment I understand
conserving mass in theory, but I am a little confused regarding, "keep the
mass-lambdas at one end-point as they can interact badly with
constraints". I am testing pmx on a two-molecule one-system I.e., G-D2K-G
and G-K2D-G in the same system. How ought I define the mass-lambdas for
this system? (nothing accurate, just an example would be great)?

Thanks
Anthony


On 01/06/2016 09:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Hannes Loeffler"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
Hannes.Loeffler at stfc.ac.uk> wrote:

>On Wed, 1 Jun 2016 07:54:56 +0000
>"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
>
>> In the tutorial, charges are off in the topology and the electrostatic
>> coupling to lambda remains 0 throughout the 20 windows. I assume
>> setting col_lambdas=0 0 0 Š was for that very reason I.e., the
>> charges were off? Could the charges not have been left on and
>> col_lambdas defined similar to vdw_lambdas?
>> (I understand that if charges remain constant, as vdw turns off, the
>> system will probably blow up as attraction brings molecules infinitely
>> close).
>
>Technically, Gromacs allows you to vary both vdW and Coulomb lambdas
>simultaneously because Gromacs can apply softcore potentials to both.
>In practice though it seems that many workers still prefer to separate
>the two terms from each other.
>
> 
>> If my transition is from a small molecule into a small molecule e.g.,
>> G-D-G to G-K-D, (the PMX paper) should I define all three lambdas:
>> vdw_lambdas, col_lambdas and bonds_lambdas? Between states A and B,
>> VdW, charges and bonds are all changing.
>
>Lambda paths are only about separating the various force field terms
>from each other.  If you do not explicitly state any of those lambda
>vectors they will adopt they same lambdas as specified in fep-lambdas,
>see manual.  I do not see a reason why you would want to separate out
>the bonded terms as well.  They are subject to a linear transformation
>only anyway.
>
>What you may want to do is to keep the mass-lambdas at one end-point as
>they can interact badly with constraints.  In a proper thermodynamic
>cycle mass contributions must perfectly cancel.
>
>
>Cheers,
>Hannes.
>-- 
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