[gmx-users] Clarity on TI free energy terms

[Nash, Anthony]

In the mean while, do you know of any tutorials (besides the methane in
water FE tutorial) regarding TI for amino acid substitution? And by
“q_off” and “vdw_on/off”, I assume you are referring to the ‘value’ of the
couple-lambda0: parameter?

Thanks
Anthony

Dr Anthony Nash
Department of Chemistry
University College London





On 01/06/2016 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of Nash, Anthony"
<gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
a.nash at ucl.ac.uk> wrote:

>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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