Practical question: why would you want to do that? Your two molecules will drift apart unless parts of the molecules are linked together in a "single" topology fashion or or you introduce other restraints/constraints.
In practice, you can do that with Gromacs relatively easily. The manual describes how to set up the A and the B state of a molecule. ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Sebastian Stolzenberg [s.stolzenb...@fu-berlin.de] Sent: 29 November 2015 13:11 To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] tutorial for "dual" alchemical transformation in gromacs? Dear Gromacs experts, I am looking for a Gromacs tutorial to perform a "dual" alchemical transformation in a water box, i.e. a mutation or any other alchemical transformation, in which: the nonbonded interactions between the environment and a molecule A disappear as lambda goes from 0 to 1, and the nonbonded interactions between the environment and a molecule B appears simultaneously. Interactions between atoms A and B are to be excluded. So far, I have been trying to use the Gromacs user guide to extend the ethanol tutorial http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf into such a "dual" transformation, but also because I am currently faced with manually manipulating my topology file, this option is highly prone to my own errors. Would you be able to help? With Thanks and Best Regards, Sebastian -- 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.
