Re: AMBER: spherical boundary condition

From: Andreas Svrcek-Seiler <svrci.tbi.univie.ac.at>
Date: Mon, 14 Mar 2005 19:36:06 +0100 (CET)

Hi,
If you restrain multiple peptides by an elastic spherical wall
outside, they might go ballistic insite the cavity, sometimes
bouncing off the wall or off each other. Are you sure you want that?
*If* you really want that, you could change the code for the harmonic
restraints (sorry - I don't know where that is in the AMBER code).
Then, setting all restraint positions (e.g.) to zero,
you'd just have to change the restraint potential to whatever you want if
|r - r0| > R_restraint , zero otherwise (and never forget to fix the
gradient).
If you want that and don't want/dare to fiddle with the fortran code,
you could try NAB
(http://www.scripps.edu/mb/case/casegr-sh-3.2.html)
instead. In this case I could simply send you the patch
and explain how to use it.

Generally, if you explain what you want to do in more detail,
more people might be able to help you.

regards
Andreas

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Received on Mon Mar 14 2005 - 18:53:01 PST