Hello,
2011/4/12 Jason Swails <jason.swails.gmail.com>
> Hello,
>
> The solvent bonded terms will necessarily be zero, since there is *no*
> dihedral parameter, and if it's a rigid water molecule, then SHAKE holds
> the
> bonds at their fixed, equilibrium distance.
>
At this stage of my research, solvent I am using is dichloromethane. As
stated before, bonding interactions in the "MM" region are 'set' to zero by
*ibelly* mask allowing only "QM" atoms to move. In that way, bonding
interactions in the "QM" region are treated in the spirit of MM philosophy.
Let's say that the bonding interactions are treated as I need them to be.
>
> On to the non-bonded interactions. As long as the water Oxygen still has a
> VDW radius, it will calculate the VDW interaction between the MM and QM
> atoms (HWs have no VDW radii). Squashing those VDW terms could be tricky,
> depending on what, exactly, you're trying to do.
> Do you care if the water molecules experience inter-molecular VDW forces?
> Or do you want to get rid of *ALL* other non-bonded interactions (such as
> MM-MM VDW interactions)?
>
What I want is to get rid of *all* VDW interactions between *all *atoms in
MM region and *all* VDW interactions between *all* "QM" and* all* "MM"
atoms. All VDW interactions I need to account for are *only* those between *
all* atoms within "QM" region.
>
> If you want to get rid of all VDW interactions, then you'll have to create
> an frcmod file like previously suggested, and set the OW atom type to have
> 0
> VDW radius/well-depth. Have a look in http://ambermd.org/formats.html,
> along with the ambertools manual to find out how to format an frcmod file.
>
> However, if all you want to do is zero out the VDW interactions between QM
> and MM atoms, then that's a bit trickier. You have to figure out how the
> LENNARD_JONES_ACOEF and LENNARD_JONES_BCOEF are indexed (by atom type,
> etc.), and zero out ONLY those terms that represent QM atom types
> interacting with MM atom types.
>
That was exactly what I was doing for the last few days. But I failed. The
problem is the following: for a solute and a solvent, antechamber module was
used to generate frcmod files. Then in leap an inpcrd and a prmtop files
were generated. What I have now is the same atom type for a carbon atom of a
dichloromethane and a carbon atom of a chromophore (the same problem is for
a hydrogen atom). So, if I modify prmtop file in a way that all non-bonded
parameters between this specific "MM" carbon atom and all other atoms are
zero, I would automatically set to zero all interactions in which a "QM"
carbon atom of the same type is included. (Is that right?) And that is not
what I want to do (I want to keep VDW interactions within QM region).
My next attempt was debug option
do_debugf=1, zerovdw=1
in combination with *ibelly* mask. In this way, I got rid off bonding
interactions in MM region (that's good), keep electrostatical interactions
of "QM" atoms with point charges of "MM" region (that's also good) and got
rid off *all* VDW interactions (that's bad, because I need VDW interactions
within QM region). Is there any way that I can include them in my
calculation? Except to run an additional calculation of QM region in the gas
phase and than add VDW energy to the one calculated with debug option on?
Or is a solution to change a code? If you think that this is the only
solution, could You please say which module should be change?
>
> One last piece of advice: I would NOT change that water atom types, since
> those are hard-coded in places in the code to recognize rigid waters; so
> you
> don't want to get rid of that.
>
> Hope this helps,
> Jason
>
Thanks in advance,
Jura
>
> On Tue, Apr 12, 2011 at 7:13 AM, Jurica Novak <jnovak.irb.hr> wrote:
>
> > Great! If in Amber's mechanical embedding QM/MM approach reported SCF
> > energy
> > includes *only* electrostatic influence of "non-QM" atoms on "QM" atoms
> > (with Ewald summation included and all bonded and non-bonded
> contributions
> > of "non-QM" atoms are exactly zero), that would be perfect. Does anyone
> > know
> > which flag(s) should be turned on for a such single point run
> > ('independent'
> > of Amber's QM/MM dynamics)?
> >
> > In case of using "NTR" keyword there is additional contribution to total
> > energy - RESTRAINT. Another option that I've tried is using *"ibelly*"
> > mask,
> > allowing only "QM" atoms to move. This helped in sense that all bonded
> > contributions of solvent molecules are exactly zero (I've compared bonded
> > contributions to energy by comparing calculations with *"ibelly*" keyword
> > on
> > and only "QM" subsystem in gas phase). But, non-bonding interactions of
> > "non-QM" atoms remain sofar as unsolved problem to me.
> >
> > Best regards,
> > Jura
> >
> > 2011/4/12 Gustavo Seabra <gustavo.seabra.gmail.com>
> >
> > > Could you describe in more detail what you want to do?
> > >
> > > In Amber's QM/MM approach, when you do a single point calculation, the
> > > SCF energy reported already includes the influence of "non-QM" atoms
> > > as point charges over the QM region. If you also turn off the periodic
> > > boundary conditions, that's all you get. Otherwise, an Ewald sum for
> > > the long range electrostatic interactions will also br included.
> > > Finally, you can look at the "NTR" and "NTF" options for sander to
> > > turn off particular terms of the force field.
> > >
> > > HTH,
> > > Gustavo.
> > >
> > > On Tuesday, April 12, 2011, Jurica Novak <jnovak.irb.hr> wrote:
> > > > Dear Amber user,
> > > >
> > > > Could anyone suggest me how to run Amber single point calculation in
> a
> > > way
> > > > that atoms of solvent are represented only as a point charges (with
> all
> > > > other interactions - bonding and nonbonding - turned off), while in
> the
> > > same
> > > > time all interactions of solute atoms are accounted for?
> > > >
> > > > Thanks in advance,
> > > >
> > > > Jura
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > > --
> > > Gustavo Seabra
> > > Professor Adjunto
> > > Departamento de Química Fundamental
> > > Universidade Federal de Pernambuco
> > > Fone: +55-81-2126-7417
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 18 2011 - 03:00:02 PDT
