[gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Hannes Loeffler
Hannes.Loeffler at stfc.ac.uk
Tue Dec 1 15:59:00 CET 2015
You still have couple-moltype set.
On Tue, 1 Dec 2015 15:39:40 +0100
Sebastian Stolzenberg <s.stolzenberg at fu-berlin.de> wrote:
> OK, thanks a lot, Hannes,
>
> I combined the "CL-" and "NA+" into one "NC" [moleculetype] and
> switched off the couple-* switches as you suggested (attached),
> but I am still receiving the same warning message:
> "The lambda=0 and lambda=1 states for coupling are identical"
>
> I guess I am almost there, am I missing something else?
>
> Thanks again,
> Sebastian
>
>
>
> On 01.12.2015 14:22, Hannes Loeffler wrote:
> > 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.Loeffler at 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.stolzenberg at 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.loeffler at 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-bounces at maillist.sys.kth.se
> >>>> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of
> >>>> Sebastian Stolzenberg [s.stolzenberg at fu-berlin.de] Sent: 30
> >>>> November 2015 16:19 To: gromacs.org_gmx-users at 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.loeffler at 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-bounces at maillist.sys.kth.se
> >>>>> [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of
> >>>>> Sebastian Stolzenberg [s.stolzenberg at fu-berlin.de] Sent: 29
> >>>>> November 2015 13:11 To:
> >>>>> gromacs.org_gmx-users at 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-request at 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
> >>>> ----------------------------------------------
> >>>>
> >>>>
> >>>
> >>>
> >>
> >
>
>
More information about the gromacs.org_gmx-users
mailing list