FIXED atoms not included as described in the documentation

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Mon Aug 13 2007 - 04:49:03 CDT

Hi,

When I run simulations with fixed atoms, they appear to be written in the
dcd file the same as if they were not fixed. The sizes of the dcd files are
the same also as the nonfixed.

The atoms are definitely fixed however

When I do a grep for 'FIXED' on the output I see this, and the energies are
definitely not being calculated I expect.

Info: FIXED ATOMS ACTIVE
Info: 2800 FIXED ATOMS
Info: 2800 HYDROGEN GROUPS WITH ALL ATOMS FIXED

The NFREAT variable (ICNTRL(9)) also is zero in the DCD file.

I also know they are fixed because I can see that they are. Is there
something special that you need to do to turn the feature on for the dcd
file to only write the coordiates of the moving atoms?

I am fixing them by doing

fixedAtoms on
fixedAtomsCol O

and then changing the occupancy column in the pdb file to be '0.00' for the
atoms I want to let move.

Thanks.

Josh

-- 
------------------------------------------------
Joshua D. Moore
Graduate Student
North Carolina State University
Dept. of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC  27695-7905
Phone: (919) 513-2051
Fax:   (919) 513-2470
Email:  jdmoore_at_unity.ncsu.edu
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