[gmx-users] tutorial for "dual" alchemical transformation in gromacs?
Hannes Loeffler
Hannes.Loeffler at stfc.ac.uk
Tue Dec 1 14:17:43 CET 2015
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
> >> --
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> >>
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> >
> >
> > --
> > ----------------------------------------------
> > 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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