From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Thu Nov 15 2007 - 10:15:17 CST
Dear Jerome, NAMD users,
I defined a new restraint in ABF which applies a linear bias on a
distance between a point (the center of mass of some atoms) and a line
(the distance between two centers of mass of some other atoms).
Basically, this applies a force that is perpendicular to the ABF bias
(rc = abscissa). The restraint force is calculated from the ABF bias in
such a way that adding the vectors of the ABF bias and the restraint
bias gives the direction of the force I want.
Currently I am applying this restraint bias continuously during the
simulation. Thus, even when the ABF bias is not applied, the restraint
bias is still active.
I have just submitted the first tests so I dont know if this produces
the result I want but looking at the output it looks OK thus far ...
I have short questions:
1. Is there any way to see how this restraint affects the calculation of
the pmf? According to the ABF manual, if the reaction coordinate is
defined considering all the atoms involved in the restrain, it should
not affect ....
2. Could you give me a short hint, how I could write in the NAMD output
the values of the restrained distance at certain time intervals
(something like the ABF output of Xi at writeXiFreq intervals ?
Thanks a lot for all the help
Best
vlad
-- ---------------------------------------------------------------------------- Dr. Vlad Cojocaru EML Research gGmbH Schloss-Wolfsbrunnenweg 33 69118 Heidelberg Tel: ++49-6221-533266 Fax: ++49-6221-533298 e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de http://projects.villa-bosch.de/mcm/people/cojocaru/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------
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