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
