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-boun...@maillist.sys.kth.se on behalf of Hannes Loeffler" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of hannes.loeff...@stfc.ac.uk> wrote: >On Wed, 1 Jun 2016 15:00:51 +0000 >"Nash, Anthony" <a.n...@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. >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.