see page 135 of the manual for the equation for the energy/force.
the weighting of this term relative to the others is set by the force
constant.
since it is a harmonic term, it will oscillate.
it's not completely clear what is oscillating- the rmsd to the
target/reference or
the rmsd to some other structure. I'm unsure because you say below
things about
values of 2.5 or 8. are you setting the target value to 8 in that case,
or setting
it to 0 with the reference structure being the one 8A from some other
structure?
both are possible but the results depend on what you're asking it to do.
Whitney Allen wrote:
> Dear Amber users,
> I would like to know the limits of targeted molecular dynamics. I have
> generated a pathway for an RNA molecule that consists of several
> intermediate structures. When I go from one structure to another that
> has an all-atom RMSD of 2.5 angstroms it converges to the reference
> structure with little perturbations. When I change calculation so that
> the structure goes to another reference structure that has a
> higher all-atom RMSD, say 8 angstroms, it does converge to the
> appropriate structure, but when I plot the RMS from the first
> structure in Ptraj I get an oscillatory damping behavior (similar to
> an underdamped mechanical system). I am using pretty small force
> constants tgtmdfrc=0.01 to tgtmdfrc=0.1 (I have tried higher values
> but it doesn't change the results) and have the tgtfitmask and
> tgtrmsmask set to include only the backbone. So now to! my questions.
> First, if 8 Angstroms is too high of an RMSD, what is considered a
> reasonable maximum value? Second, what causes the oscillations, I have
> tried multiple variations of tgtmdfrc, tgtmdrms, and RMSD values
> between intermediate structures and still get this pattern. Little is
> written on how the forces generated from targeted MD are weighted in
> with the other forces used to create a trajectory. Since the molecule
> does converge to the correct structure, is this oscillatory behavior
> considered to be okay? Please help me understand the basics of
> targeted MD. Below is a sample input code.
> Thanks
> Whitney
>
> cat <<eof > mdin
> equilibrate the structure
> &cntrl
> imin=0, ntx=5,
> irest=1, ntxo=1,cut=15.0, tempi=300.0,
> ntpr=100, ntwx=100, ntwe=1000,
> nstlim=2000000,tautp=2, temp0=300.0,
> dt=0.001, nscm=100,
> igb=1,ntb=0, saltcon=0.5, gbsa=1,
> ntt=1, nsnb=20,offset=0.13,
> itgtmd=1, tgtrmsd=0.5, tgtmdfrc=0.01,
> tgtfitmask=":1-76.P,O1P,O2P,O5',O4',O3',O2',C5',C4',C3',C2',C1'",
> tgtrmsmask=":1-76.P,O1P,O2P,O5',O4',O3',O2',C5',C4',C3',C2',C1'",
> &end
> Group for target
> RES 1 76
> END
> END
> eof
>
>
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Received on Wed Nov 30 2005 - 17:53:01 PST
