[gmx-users] Clarity on TI free energy terms

[Nash, Anthony]

Dear Hannes, please see my comment below..


On 01/06/2016 14:45, "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 12:06:20 +0000
>"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
>
>> vdw_lambdas              = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35
>> 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
>> mass_lambdas = 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>> 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0
>> fep_lambdas =  0.0 0.1 0.1 0.2 0.2 0.3 0.3 0.4 0.4 0.5 0.5 0.6 0.6
>> 0.7 0.7 0.8 0.8 0.9 0.9 1.0 1.0
>
>This will transform both vdW _and_ Coulomb terms at the same time but
>at a different pace.  Maybe you want something like
>
>fep-lambdas = 0.0 0.2 0.4 0.6 0.8 1.0  1.0  1.0  etc.
>vdw-lambdas = 0.0 0.0 0.0 0.0 0.0 0.0  0.05 0.10 etc.
>mass-lambdas as above
>
>This will first transform Coulomb and bonded terms in the first six
>lambdas and vdW from the 7th lambda onwards.


That is beginning to make perfect sense now. Many thanks for that help.



>  This also assumes that
>you have vanishing atoms only.  If you have appearing atoms only you
>would obviously have to revers the order, and when you have both you
>will have to run with two mdp/tpr setups.


With aspartic acid transforming into lysine on one polypeptide chain and
then lysine transforming into aspartic acid polypeptide chain, all in the
same system (keeps the charges the same and is a complete thermodynamic
cycle), I will have both appearing and disappearing atoms. How do you mean
³to run with two mdp/tpr setups²? Is there an example you could give
(which I am grateful for) or one in the manual?


>> couple-moltype           = protein
>> couple-lambda0           = vdw-q
>> couple-lambda1           = vdw-q
>
>This will decouple all atoms in the 'protein' selection from the
>environment.  This is for absolute transformation and not what you seem
>to want to do i.e. a relative transformation of one residue into
>another.  So avoid those parameters.

Thanks for that information.


Many thanks
Anthony