From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Tue Dec 18 2007 - 10:40:39 CST
Dear Vlad,
An easy way to "stitch" together the different windows is to run a final simulation (can be very short) with abf01.out, abf02.out and abf03.out as abf inFiles and the RC spanning the full range 0-15 A.
Vaithee
---- Original message ----
>Date: Tue, 18 Dec 2007 15:01:55 +0100
>From: Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>
>Subject: namd-l: ABF: split reaction coordinate in widows
>To: NAMD list <namd-l_at_ks.uiuc.edu>
>
>Dear NAMD users,
>
>I am perfroming an ABF simulation with a reaction coordinate ranging
>from 15 to 0 A. I performed ABF simulations for 3 different windows for
>the ranges: (i) 15 to 10 A; (ii) 10 to 5 A); (iii) 5 to 0 A. For each
>range, I have the output abf01.out, abf02.out and abf03.out. My question
>is how to reconstitute the PMF for the entire range of the reaction
>coordinate from these 3 =output files covering the three non-overlapping
>regions?
>
>My initial naive guess, would be to add the value of the last bin from
>file abf01.dat to all values in abf02.dat and then the value of the last
>bin from the resulted file to each value in the abf03.dat. I am not sure
>whether this is a correct guess, though ..
>
>Thanks for answering
>
>Best wishes
>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
>----------------------------------------------------------------------------
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:42 CST