AMBER Archive (2009)

Subject: Re: [AMBER] difference in temperature

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Wed May 06 2009 - 07:29:48 CDT

These are are commands I use for getting the eigenvalue and
eigenvectors: matrix
mwcovar ...
analyze matrix ...

So these are quasiharmonic modes. But the issue isn't that the values are
different from different simulations. I completely expect that. What I have
done is write the trajectories to a file using lower precision ASCII and
later netcdf (with ~19 digit of precision) file formats. For 293 K it makes
no difference how the trajectories are written to file. The resulting
eigenvalues and eigenvectors are the same. However, when 300 K is used,
there is a difference in eigenvalues and eigenvectors when netcdf or ASCII
file formats are used. I was wondering whether this is to be expected. I
have tried this same exercise with a different molecule and with the same
results.

On Wed, May 6, 2009 at 8:08 AM, David A. Case <case_at_biomaps.rutgers.edu>wrote:

> On Tue, May 05, 2009, Naser Alijabbari wrote:
> >
> > Below are the some of the eigenvectors for the second eigenfrequency from
> a
> > MD simulation of E. coli’s thioredoxin. This is using AMBER10 running on
> Duo
> > Core EM64T processor (serial simulation), with explicit solvation (8
> > angstrom water shell, and 10 angstrom cutoff). There is very little
> > difference between eigenvalues and eigenvectors when the temperature is
> 293K
> > but there is a noticeable difference when 300K is used.
>
> It's not clear what you did here. Are these quasi-harmonic modes? It is
> not
> unusual that eigenvectors would be quite different with different
> simulations:
> even if there is a conserved set of low-frequency motions, they would tend
> to
> exchange among themselves, so that indiviudal eigenvector componenets would
> change a lot from one simulation to the next.
>
> > &cntrl
> > imin = 0, irest = 1, ntx = 5,
> > ntb = 1,
> > cut = 10, ntr = 0,
> > ntc = 2, ntf = 2, tol=.000001,
> > tempi = 293.0, temp0 = 293.0, (these are 300K for 300K simulations)
> > ntt = 0, nscm=0,
>
> Note that with irest=1 and ntt=0, the values of tempi and temp0 are
> ignored.
> You would need to examine the outputs to see what temperature you really
> have.
>
> I also note that you have changed the defaults for a number of variables,
> such
> as tol, dsum_tol, skinnb, etc. As the manual states, the defaults are
> carefully chosen to be appropriate for most simulations. If you don't have
> a
> good reason to do so, don't change them (especially by making the
> tolerances
> less tight...)
>
> ...dac
>
>
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