[gmx-users] Clarity on TI free energy terms

[Nash, Anthony]

Thanks for all of this material. I’ll take some time and digest what
you’ve said. 

No doubt I’ll have a few more questions tomorrow ;-)

Thanks
Anthony 


On 01/06/2016 16:38, "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 15:00:51 +0000
>"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
>
>> >  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?
>
>Lambda paths are not selective in the sense that you could apply them
>to only a subset of the system.  So if you have both disappearing and
>appearing atoms you have to:
>1) turn off the charges on the disappearing group (or alternatively all
>charges to avoid a charged total system), q_off
>2) turn off the vdW parameters for the disappearing group, vdw_off
>3) turn on the vdW parameters for the appearing group, vdw_on
>4) turn on the charges of the appearing group (or all charges), q_on
>
>If you try to do this with Gromacs you will realise that the best you
>can do is combine this into 2 mdp steps: 1) q_off and vdw_on/off and 2)
>q_on.  Alternatively you can combine the vdw bit with 2) but that
>doesn't make any difference.  Of course, if you could assume that a
>combined Coulomb/vdW transformation will work, this would be a
>non-issue...
>
>Also, I wonder how pmx maps aspartate onto lysine.  I would think that
>the gamma-carboxylate should not map onto the gamma-methylene but
>rather the residue should be branched off at the C-beta and so
>duplicate the rest of the residue.
>-- 
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