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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