On Thu, Mar 09, 2000, Marios Philippopoulos wrote:
> Does IBELLY really freeze the cartesian coordinates of the specified
> groups during dynamics?
Ibelly artificially sets to zero the forces on all of the atoms in the
fixed portion at the end of each energy/force evaluation..
If the restart file has non-zero velocities for those atoms, then things
could go quite badly wrong. I suppose that one should artificially set
all the velocity components to zero as well, etc.
A problem is that none of the (current) principal developers ever use
this option....what is needed is for someone to carefully look at all of
the implications of trying to completely freeze certain groups. For
the present, it might be better to use "ntr" (if you can), rather than
"ibelly".
...good luck...dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
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Received on Thu Mar 09 2000 - 10:25:33 PST
