AMBER Archive (2009)

Subject: [AMBER] ntf, ntc with softcore potentials and TI in amber10

From: Matthew Wilce (Matthew.Wilce_at_med.monash.edu.au)
Date: Tue May 05 2009 - 20:33:28 CDT

Dear Amber experts,
I have found that I am unable to use ntf=2, ntc=2 with ifsc=1 during
thermodynamic intergration (as in step 2 of the TI tutorial). I had
perhaps naively thought that using scmask would allow ntf=2,ntc=2 and
that scmask would exclude those atoms with softcore potentials from
SHAKE.

So I guess I am really asking - whether the above is correct? and, do
I need to use ntf=1,ntc=1 with softcore potentials. Does this matter,
keeping in mind that ntf=2,ntc=2 are used during charge removal and
then addition (as in step1 and step3 of the TI tutorial)

Cheers,
Matthew

Matthew CJ Wilce
NHMRC Senior Research Fellow
Department of Biochemistry & Molecular Biology
Building 76, Monash University
Tel: +61-3-9902-9244

Email: matthew.wilce_at_med.monash.edu.au

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