Ok, my attachment seems to have been stripped, so inline only. Hope it's not too bad.
[ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb DU DU 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 OW OW 0.00000 0.00000 A 3.15075e-01 6.35968e-01 ; 1.77 0.1520 HW HW 0.00000 0.00000 A 0.00000e+00 0.00000e+00 ; 0.00 0.0000 [ moleculetype ] ; molname nrexcl NA+CL- 1 [ atoms ] ; DU->IP ; IM->DU ; = IM->IP ; id_ at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 DU 1 NA+ NA+ 1 0 22.9898 IP 0 22.9898 2 IM 1 DU DU 2 0 35.4530 DU 0 35.4530 On Tue, 1 Dec 2015 13:17:38 +0000 Hannes Loeffler <hannes.loeff...@stfc.ac.uk> wrote: > Dear Sebastian, > > I have got your attachment. I do not know all intricacies of Gromacs > but for relative free energies you only use one moleculetype for the > perturbed group, see attachment. You do not use the couple-* switches > for relative simulations. > > Yes, you are right about typeA and typeB. If you have larger > molecules you would just combine both molecules in their entirety > into one "pseudo" molecules. One original molecules has the normal > force field types in the A state and dummy atoms in the final, while > the other molecule has this reversed. > > > Cheers, > Hannes. > > > > On Tue, 1 Dec 2015 13:34:12 +0100 > Sebastian Stolzenberg <s.stolzenb...@fu-berlin.de> wrote: > > > Dear Hannes, > > > > > I have some trouble reading your top file in my web browser > > Apologies, am not sure if this works in this list, but I am now also > > attaching my topol.top and grompp.mdp files. > > I hope this let's you see better what I am doing wrong. > > > > > As your two dummy types appear to be identical > > > you can define just one. > > Thank you, as you can see in topol.top, I now have only one dummy > > atom type called "XX". > > > > > I think your transformations are IPX->Na+, IMX->Cl-. > > my "typeA" columns are "XX" and "IM" (NA+) > > my "typeB" columns are "IM" and "XX" (CL-) > > If I understand correctly (do I?), lambda=0 corresponds to "typeA", > > whereas lambda=1 corresponds to "typeB", so my transformation is > > "XX" -> "Na+", "Cl-" -> "XX" > > > > Thanks a bunch, > > Sebastian > > > > > > > > On 30.11.2015 17:30, hannes.loeff...@stfc.ac.uk wrote: > > > Dear Sebastian, > > > > > > I have some trouble reading your top file in my web browser but I > > > think your transformations are IPX->Na+, IMX->Cl-. So you would > > > have to reverse the columns for the first atom. As your two dummy > > > types appear to be identical you can define just one. > > > > > > Cheers, > > > Hannes. > > > > > > ________________________________________ > > > 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: 30 > > > November 2015 16:19 To: gromacs.org_gmx-users@maillist.sys.kth.se > > > Subject: Re: [gmx-users] tutorial for "dual" alchemical > > > transformation in gromacs? > > > > > > 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 > > > ---------------------------------------------- > > > > > > > > > > > -- 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.