Re: ABF restrain

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Thu Jul 05 2007 - 13:05:30 CDT

Alex,

from the perspective of ABF, there are harmonic walls that prevent
sampling along the RC to "spill out" beyond the frontiers defined
by XiMin and XiMax. These walls are controlled by the keyword
"forceConst", the force constant applied at the borders of the
RC. The ABF module also allows you to include a set of additional
restraints. You might want to check the "Free Energy of Conformational
Change Calculations" section of the NAMD user's guide as well, which
will provide extra tips for enforcing restraints in your system.

Chris Chipot

alex digenova bravo a écrit :
> thank you Chris,
> How can I use "Harmonic walls" in namd?.
> thank you all.
>
> good bye
>
> Alex Di Genova Bravo.

_______________________________________________________________________

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
Nancy Université Phone: +33 (0)3-83-68-40-97
B.P. 239 Fax: +33 (0)3-83-68-43-87
54506 Vandœuvre-lès-Nancy Cedex

                             E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
                                            http://www.edam.uhp-nancy.fr

     Science without management is worse than management without science

                                                        N. G. van Kampen
_______________________________________________________________________

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