I am using my previous emails as follow up for this as it is related to the
same set up .
I used atomic fluctuations to get the changes in conformation of a planar
structure. I would like to know the values of atomic fluctuations which I
get are w.r.t which axes (x,y,z) or is it (x^2+y^2+z^2) .
Is atomic fluctuations calculations , will be best to get the changes in
planarity of the rings in my structure.
Thanks
John
On Wed, Nov 24, 2010 at 6:22 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> it really depends on what you want to calculate and what experimental data
> you are using for comparison.
> if you want a real diffusion constant, you cannot change the coordinates by
> anything other than the dynamics. you can still calculate many things, such
> as positional fluctuations or many types of NMR observables. I'm not sure I
> know what the diffusion constant of each residue would be useful for doing.
> On Tue, Nov 23, 2010 at 9:13 PM, John S <s.john634.gmail.com> wrote:
>
> > In the amber manual it says "For periodic systems,just the translational
> > center-of-mass motion will be removed."As I understand it is for the
> > entire
> > system similar to the command we use to center our trajectory in ptraj
> .So
> > will any kind of analysis of results will be affected with use of nscm .
> > I am also calculating binding energy for the same .
> > It is like my present trajectory will be of no use in calculation of any
> > kind of movement ; like occupancy and deviation of residues.
> >
> > As I was having a high temperature annealing run and then cooling it to
> > 300K, where I analyze my results; due to the high temperature run I used
> > ncsm.Was I wrong here.
> >
> > Thanks
> > John
> >
> > On Tue, Nov 23, 2010 at 6:42 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> > > I do not think you will get meaningful results for diffusion
> constants.
> > you
> > > are using nscm, which removes part of the motion. your diffusion
> > constants
> > > are non-physical.
> > >
> > >
> > > On Tue, Nov 23, 2010 at 6:04 PM, John S <s.john634.gmail.com> wrote:
> > >
> > > > Thank You for your suggestion.I can use atomicfluct to get the
> > deviation
> > > > from the the average structure.
> > > > Here I need to calculate the diffusion coefficients of selected
> > residues
> > > > too
> > > > .
> > > > So I plan to calculate this from the slope of Mean Square Deviation
> > plots
> > > > over the a selected part of trajectory (which is a range of 5000ps).
> > > >
> > > > I am not calculating diffusion of solvent , but of selected residues
> of
> > > my
> > > > structure (in all 5 residues).
> > > > Yes the MSD trajectory is noisy, will I get meaningful results out of
> > > this
> > > > analysis of diffusion coefficients
> > > >
> > > > Thanks
> > > > John
> > > >
> > > > On Tue, Nov 23, 2010 at 4:40 PM, Thomas Cheatham III <tec3.utah.edu>
> > > > wrote:
> > > >
> > > > >
> > > > > > To be more clear ,I am calculating as below,
> > > > > >
> > > > > > trjain md.x 4 40000 4
> > > > > > strip :64-200
> > > > > > diffusion :1 1 res1
> > > > > > diffusion :2 1 res2
> > > > >
> > > > > If you are trying to calculate mean-squared-displacement (which is
> > > > related
> > > > > to the diffusion coefficient) as opposed to root-mean-squared
> > deviation
> > > > > (which is what Simmerling was referring to) you want to use the
> > > diffusion
> > > > > command. You definately do not want to do any RMS fitting since
> this
> > > > best
> > > > > fits the coordinates via rotation/translation and will remove the
> net
> > > > > displacement. There is also no need to strip any coordinates for
> > this
> > > > > calculation.
> > > > >
> > > > > Note that the MSD for a single residue will be rather noisy; to get
> > > > > reasonable diffusion coefficients for a solvent it is much better
> to
> > > > > average over all the solvent than you follow an individual solvent
> > > > > molecule. Tracking an individual residue will likely, except if
> done
> > > as
> > > > > an ensemble average over multiple trajectories, not provide much
> > useful
> > > > > information except to suggest that one residue moves "more" than
> > > another.
> > > > >
> > > > > Now maybe you do not want the mean-squared displacement but instead
> > > want
> > > > > the atomic (or residue) positional fluctuations, such as a
> B-factor.
> > > For
> > > > > that use the atomicfluct command and note that in this case, you
> > likely
> > > > > want to fit the trajectory to an average structure first to get the
> > > > > fluctuations about the average structure...
> > > > >
> > > > > --tec3
> > > > >
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Received on Thu Dec 09 2010 - 15:00:02 PST
