It seems like a flat-well potential would suit better here. You can
effectively use a distance restraint with a flat-well potential like a
spherical well to keep the CO2 molecule inside a region of spaced defined
with respect to the center of mass of a particular set of atoms.
With a flat-well potential, you can make it so there is no penalty for
staying within, say, 5 Angstroms of a given point in space (defined
relative to your system, so this restraint is immune to
translations/rotations, unlike, say, positional restraints). After this,
the penalty becomes quadratic (and eventually linear). Look at the nmropt
option (and NMR restraints in the manual).
Targeted MD does not seem to be the right choice, in part because you are
affecting your system a lot simply to keep the CO2 molecules localized.
The flat-well potential is a far smaller perturbation (and it allows you
to run with pmemd and pmemd.cuda, too).
It is important to be able to defend what you are doing and anticipate ways
in which your settings may affect the system and bias your results. Also
think about what question you are asking and how your simulation will (or,
even better, would NOT) work to answer that question. For instance, you
can't design a simulation aimed at forcing CO2 to stay in a particular
region inside the protein and then claim you've found the CO2 binding
pockets.
Ultimately, however, all of this is speculation. Nobody can answer these
questions better than the simulations themselves, and I encourage you to
allow some more time between repeats of the same email (and even consider
that nobody may have the answer to your question). It will most likely
only frustrate the people whose help you want.
Good luck,
Jason
On Fri, Feb 1, 2013 at 5:59 PM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Hi all,
>
> I would be highly obliged if you could please look into this. I can run my
> calculation with this set up and see what happens, I just wanted to get the
> set up perused and may be get modified by your expertise.
>
> Thank you
>
> Sajeewa Dewage
>
> ---------- Forwarded message ----------
> From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
> Date: Thu, Jan 31, 2013 at 1:03 PM
> Subject: Sampling of a point by a molecule while keeping the relative
> position of the molecule unchanged in TMD
> To: AMBER Mailing List <amber.ambermd.org>
>
>
> Hi all,
>
> I have some CO2 molecules placed at particular , pre-determined points
> inside a protein. I want to sample the positions of CO2 molecules around
> those particular points while keeping their relative position with respect
> to the surrounding of each CO2 as constant as possible. When I went through
> the description of the technique in the AMBER manual I thought targeted MD
> would serve the purpose coz it allows to give a set of atoms as a reference
> and restrain the motion of the atoms, in terms of RMSD while the simulation
> is going on.
>
> Letz say that the residue numbers that I use as surrounding for a
> particular CO2 are 410, 385, 835, 525 and the residue number of the
> particular CO2 is 902
>
> If I have an mdin file like below, will it serve my purpose(i.e to keep the
> position of the residue 902 more or less constant with respect to the
> surrounding while having my initial protein.prmcrd file as the reference in
> *-ref*)?
>
> TMD
> &cntrl
> ntx=1,irest=0,
> nsnb=1,ntpr=5,ntwx=100,nstlim=500000,dt=0.001,
> ntc=2,ntf=2,ntb=1,iwrap=1,
> ntt=3,temp0=300,tempi=300,gamma_ln=4,ig=10502,
> cut=8.0,
> igtmd=1,tgtfitmask=':410,385,835,525,902',
> tgtrmsmask=':410,385,835,525,902', tgtrmsd=0.0, tgtmdfrc=1.0,
> /
>
> Please suggest if any modifications are required. And about the force
> constant(tgtmdfrc=1.0), should I apply a higher force constant? If so like
> how much?
>
> Thank you very much
>
> Sajeewa Dewage
> _______________________________________________
> 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
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Received on Fri Feb 01 2013 - 19:30:02 PST
