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-boun...@maillist.sys.kth.se on behalf of Nash, Anthony" <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of a.n...@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-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. -- 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.