[gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Hannes Loeffler
Hannes.Loeffler at stfc.ac.uk
Tue Dec 1 14:22:39 CET 2015
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!
> > >>
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> > >> 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
> > > ----------------------------------------------
> > >
> > >
> >
> >
>
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