Questions about thermodynamic integration in NAMD 2.7b2

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Mon Feb 01 2010 - 14:27:22 CST

I have a couple of questions regarding the implementation of
thermodynamic integration (TI) in NAMD 2.7b2.

The first is regarding the use of alchLambda and alchLambda2:
In the users guide example on TI, only alchLambda is listed, but NAMD
complains that alchLambda2 is necessary. Adding alchLambda2 for each
alchLambda value allows the TI calculation to run, and doesn't seem to
affect the results, but I'm worried that I'm missing something.

The second deals with the script namd2_ti.pl:
The script works fine for cases where alchElecLambdaStart 0.0, however,
for non-zero values of alchElecLambdaStart, the script spits an error:
Reading files: .Modification of non-creatable array value attempted,
subscript -9 at ./namd2_ti.pl line 102, <FILE> line 309.

This error disappears if I include all of the equilibration data, so it
appears linked to the handling of this data. I looked through the
script briefly, but I don't have much experience with perl. Does anyone
have a workaround or a fix for this situation?
Regards,
    Jeff

-- 
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Jeffrey J. Potoff                         jpotoff_at_chem1.eng.wayne.edu
Associate Professor                       Wayne State University		
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815
http://potoff1.eng.wayne.edu
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