Re: [AMBER] NVT Vs NPT MD simulations

From: Mahmoud Soliman <mahmoudelkot.gmail.com>
Date: Wed, 16 Mar 2011 17:00:46 +0200

   Dear guys,
   I am running MD simulation for an enzyme in a water box. Normally, during
   heating and equilibration of the system I impose some restraints on some
   residues and I use NVT during that. But in production, I do not put any
   restraints and I use NPT. Actually, I learn that from amber tutorials but I
   see some papers adopting NVT during the production phase... So can you guys
   provide me with your experience about merits/drawbacks of both protocols
   (NVT and NPT)...much appreciated! Also do you have like a typical procedure
   for equilibration and then production run that you experience that it works
   well with ligand-enzyme complex systems
   Best wishes
   Mahmoud

   --

   *************************************************

   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath

   Bath

   BA2 7AY

   United Kingdom

   [1]http://people.bath.ac.uk/mess20/

   [2]http://www.bath.ac.uk/person/812559


   *********************************************

   Mahmoud E. Soliman

   Lecturer of pharmaceutical organic chemistry

   Pharmaceutical Organic Chemistry Dept.

   Faculty of pharmacy

   Zagazig University

   Zagazig

   Egypt

   **********************************************

   Email:

   [3]mess20.bath.ac.uk

   [4]meelkot.zu.edu.eg

   [5]mahmoudelkot.gmail.com


   --

   *************************************************

   Mahmoud E. Soliman

   Computational Chemistry & Modeling (PhD)

   Department of Chemistry

   University of Bath

   Bath

   BA2 7AY

   United Kingdom

   [6]http://people.bath.ac.uk/mess20/

   [7]http://www.bath.ac.uk/person/812559


   *********************************************

   Mahmoud E. Soliman

   Lecturer of pharmaceutical organic chemistry

   Pharmaceutical Organic Chemistry Dept.

   Faculty of pharmacy

   Zagazig University

   Zagazig

   Egypt

   **********************************************

   Email:

   [8]mess20.bath.ac.uk

   [9]meelkot.zu.edu.eg

   [10]mahmoudelkot.gmail.com

References

   1. http://people.bath.ac.uk/mess20/
   2. http://www.bath.ac.uk/person/812559
   3. mailto:mess20.bath.ac.uk
   4. mailto:meelkot.zu.edu.eg
   5. mailto:mahmoudelkot.gmail.com
   6. http://people.bath.ac.uk/mess20/
   7. http://www.bath.ac.uk/person/812559
   8. mailto:mess20.bath.ac.uk
   9. mailto:meelkot.zu.edu.eg
  10. mailto:mahmoudelkot.gmail.com
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Received on Wed Mar 16 2011 - 08:00:07 PDT
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