ABF with the RMSD colvar

From: George Patargias (gpat_at_bioacademy.gr)
Date: Tue Apr 15 2014 - 05:22:46 CDT

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Hello,

I am trying to set up an ABF calculation using the RMSD colvar. The atom
block of the colvar configuration file contains all the C-alpha atoms of a
protein complex that consists of 7 (non covalently linked) subunits.

I am trying to decide whether I need to exclude the wrapAll option (and
use only wrapWater) on the basis of the recommendations found here

http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132410000000000000

I would really appreciate any tips on this

Thanks!

Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568

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