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 > ---------------------------------------------- > > -- ---------------------------------------------- Sebastian Stolzenberg, Ph.D. PostDoc, Computational Molecular Biology group Freie Universität Berlin Phone: (+49) (0)30 838 75153 Mail: Arnimallee 6, 14195 Berlin, Germany ----------------------------------------------
; in.amber_GMX.top created by acpype (Rev: 8810) on Mon Nov 30 15:20:20 2015 [ defaults ] ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 0.5 0.8333 [ 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 XX IP 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+ 1 [ atoms ] ; id_ at type res nr residu name at name cg nr charge mass typeB chargeB massB 1 XX 1 NA+ NA+ 1 0 22.9898 IP 0 22.9898 [ moleculetype ] ; molname nrexcl CL- 1 [ 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 XX 0 35.45300 [ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834 16.00000 2 HW 1 WAT H1 1 0.417 1.00800 3 HW 1 WAT H2 1 0.417 1.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 0.09572 462750.4 1 3 1 0.09572 462750.4 0.09572 462750.4 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.520 836.800 104.520 836.800 #else [ settles ] ; i j funct length 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif [ system ] in.amber [ molecules ] ; Compound nmols NA+ 1 CL- 1 WAT 414
; we'll use the sd integrator with 100000 time steps (200ps) integrator = sd nsteps = 100000 dt = 0.002 nstenergy = 1000 nstlog = 5000 ; turn off trajectory writing nstxout = 0 nstvout = 0 ; We use the old group scheme because as of writing, the Verlet scheme ; does not support free energy calculations with coupled molecules. cutoff-scheme = group ; cut-offs at 1.0nm rlist = 1.0 dispcorr = EnerPres vdw-type = cut-off rvdw = 1.0 ; Coulomb interactions coulombtype = pme rcoulomb = 1.0 fourierspacing = 0.12 ; Constraints constraints = all-bonds ; set temperature to 300K tcoupl = v-rescale tc-grps = system tau-t = 0.2 ref-t = 300 ; set pressure to 1 bar with a thermostat that gives a correct ; thermodynamic ensemble pcoupl = parrinello-rahman ref-p = 1 compressibility = 4.5e-5 tau-p = 5 ; energygrp-excl = Cys Ser ; freezegrps = Cys Ser ; freezedim = Y Y Y Y Y Y ; and set the free energy parameters free-energy = yes couple-moltype = NA+ CL- ; these 'soft-core' parameters make sure we never get overlapping ; charges as lambda goes to 0 sc-power = 1 sc-sigma = 0.3 sc-alpha = 1.0 ; we still want the molecule to interact with itself at lambda=0 couple-intramol = yes ; couple-lambda1 = vdwq ; couple-lambda0 = vdwq init-lambda-state = 0 ; These are the lambda states at which we simulate ; for separate LJ and Coulomb decoupling, use fep-lambdas = 0.0 0.2 0.4 0.6 0.8 0.9 1.0
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