[gmx-users] Clarity on TI free energy terms

[Hannes Loeffler]

Set the vector to all-zeroes (or ones).


On Wed, 1 Jun 2016 09:47:59 +0000
"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:

> 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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