Hi everyone:
I'm forwarding Peter's suggestions, slightly reformatted to highlight three
possible improvements. Volunteers are welcome!
...dac
----- Forwarded message from Peter Varnai <p.varnai.sussex.ac.uk> -----
Date: Thu, 20 Aug 2009 16:23:48 +0100
From: Peter Varnai <p.varnai.sussex.ac.uk>
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Distance restraint and periodic boundary conditions
Thanks for your response. It is hard to avoid the need to use nmropt
with iwrap when one does umbrella sampling in explicit water for 100ns<.
(1) I think binary restart files (ntxo=0) are no longer allowed (amber10).
It would be good to re-enact this option though.
(2) Until then I wonder if some tweak could force iwrap to
consider the complexed molecules as one: pmemd has a variable
"no_intermolecular_bonds" which could redefine the complex as one fused
molecule if I introduced some covalent linkage (with zero force constant)
between the subunits.
(3) To correct my restart files with separated subunits (to continue
simulation) I will use ptraj and image the subunits back to a complex,
write out this restart file and then paste the velocities from the old
restart file... would be nice if ptraj could also dump the velocities from
the restart file after imaging.
Peter
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Received on Fri Aug 21 2009 - 05:11:33 PDT
