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 Wed Nov 24 2010 - 03:30:03 PST
