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.