Dear Hannes, Thank you very much for your answer.
> 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. I am doing some method development, so my plan is to currently fix all atoms of A and B. > 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. OK, thanks. As a start, I set up a simple "Cl->Na in a water box" system: gro file: 1 Na+ NA+ 1 1.434 1.045 1.049 2 Cl- CL- 2 1.434 1.045 1.049 3 WAT O 3 2.914 1.241 1.997 3 WAT H1 4 2.899 1.335 1.984 3 WAT H2 5 2.841 1.212 2.052 ... i.e., I transform a "Cl-" into a "Na+" by de-coupling (annihiliating) the non-bonded interactions of "Cl-" and coupling (letting appear) the ones for "Na+". This I attempt by defining "dummy" atom types IMX and IPX for Cl- and Na+, respectively: top file: ... [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb IP IP 0.00000 0.00000 A 3.32840e-01 1.15897e-02 ; 1.87 0.0028 IM IM 0.00000 0.00000 A 4.40104e-01 4.18400e-01 ; 2.47 0.1000 IPX IP 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 IMX IM 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 ... [ atoms ] ; id_ at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 IPX 1 NA+ NA+ 1 0 22.9898 IP 0 22.9898 ... [ atoms ] ; id_ at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 IM 1 CL- CL- 1 0 35.45300 IMX 0 35.45300 (Please note that for now, I artificially set the charge of each ion to zero to avoid total charge differences for different lambda values. Also, for "Cl->Na", this strategy is certainly more complicated, but in principle allows for different numbers of atoms between molecule A and B in the "A->B" transformation.) Unfortunately, running grompp with the standard run.mdp file from http://www.gromacs.org/@api/deki/files/196/=fe-tutorial-4.6.pdf (I omitted "couple-lambda0" and "couple-lambda1" and set "couple-moltype = NA+ CL-") I am puzzled by the following error message: "The lambda=0 and lambda=1 states for coupling are identical" Is it possible from this error message to see what I am doing wrong? Many Thanks, Sebastian On 29.11.2015 14:36, hannes.loeff...@stfc.ac.uk wrote: > 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. > -- ---------------------------------------------- Sebastian Stolzenberg, Ph.D. PostDoc, Computational Molecular Biology group Freie Universität Berlin Phone: (+49) (0)30 838 75153 Mail: Arnimallee 6, 14195 Berlin, Germany ----------------------------------------------
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