From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Mon Apr 26 2004 - 09:11:34 CDT
Hi Michael,
I did not find an 'xst' file, but there is an 'xsc' file with this
info:
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z
s_u s_v s_w
600000 57.0341 0 0 0 29.1591 0 0 0 29.8839 -0.14305 0.47288 0.31587
-1.43536e-05 -1.43536e-05 -1.43536e-05 0 0 0
So the volume is ~49,698.8 angstroms^3. Which is now in agreement with
the final output in .log.
Do I need to put these new cell basis vectors into the configuration
file by hand? or does NAMD automatically read them in upon continuation
of the trajectory?
Also there is still a discrepency between the cell volumes measured
through vmd and the one stated in 'xsc'.
Here is what vmd measures from the last output to '.coor':
vmd > set water [atomselect top water]
atomselect0
vmd > measure minmax $water
{-28.9479999542 -14.6990003586 -15.3159999847} {29.0540008545
15.6199998856 15.6979999542
=> ~54,504 ang^3
and the cell origin changes to (according to vmd):
-0.210047319531 0.705947160721 0.297380447388
I believe the 'xsc' file and '.coor' file contain info on the same
snapshot, they appear to be written out at the same time.
I'm missing something, though I don't know what it is!
Ed
> On Sun, 25 Apr 2004, Michael Grabe wrote:
>
> > Edward,
> >
> > What volume did the xst file give?
> > This should be the only file that you need
> > when restarting a run so that the cell basis
> > vectors are correct.
> >
> > -michael
> >
> > On Apr 25, 2004, at 10:56 AM, Edward Patrick Obrien wrote:
> >
> > > .coor file into vmd and calcu
> > ------------------------------------------------------------------------
> > --------------------------
> > Michael Grabe, Ph.D.
> > Post-doctoral Fellow
> > Howard Hughes Medical Institute
> > University of California, San Francisco
> > 1550 4th Street GD482
> > San Francisco, CA 94143
> > mgrabe_at_itsa.ucsf.edu
> > tel: ++ 415.476.4021
> > http://itsa.ucsf.edu/~mgrabe
> >
> >
>
>
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