Dear Jason,
Thanks for the precious information so far. It actually helps!
Best wishes
Mahmoud
On 3/16/11 6:49 PM, Jason Swails wrote:
Hello,
I'll share my opinion, which may differ from others. NPT is very useful for
equilibrating density, and can relieve artifacts arising due to the fact
that the system may not have been optimally packed to begin with (which is
the case for tleap-created systems). If you do not run with NPT at all (and
just NVT), then you wind up bubbles appear as the water retracts into its
*normal* density in the liquid phase.
Thus, during equilibration, NPT is quite useful to maintain a constant
density and let the box reduce to the "proper" size for the number of
solvent molecules in your system. However, NPT is more expensive than NVT
because the pressure scaling is not free. Therefore, many people use NVT
after they've equilibrated at NPT. Solvent (i.e. water) is largely
incompressible, so NVT and NPT are, for all intents and purposes, equivalent
(for an equilibrated system).
Hope this helps,
Jason
On Wed, Mar 16, 2011 at 12:31 AM, Mahmoud Soliman [1]<mahmoudelkot.gmail.com>wr
ote:
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!
Best wishes
Mahmoud
--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[1][2]
http://people.bath.ac.uk/mess20/
[2][3]
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:
[[4]3]mess20.bath.ac.uk
[[5]4]meelkot.zu.edu.eg
[[6]5]mahmoudelkot.gmail.com
References
1. [7]
http://people.bath.ac.uk/mess20/
2. [8]
http://www.bath.ac.uk/person/812559
3. [9]mailto:mess20.bath.ac.uk
4. [10]mailto:meelkot.zu.edu.eg
5. [11]mailto:mahmoudelkot.gmail.com
_______________________________________________
AMBER mailing list
[12]AMBER.ambermd.org
[13]
http://lists.ambermd.org/mailman/listinfo/amber
--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[14]
http://people.bath.ac.uk/mess20/
[15]
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:
[16]mess20.bath.ac.uk
[17]meelkot.zu.edu.eg
[18]mahmoudelkot.gmail.com
References
1. mailto:mahmoudelkot.gmail.com
2.
http://people.bath.ac.uk/mess20/
3.
http://www.bath.ac.uk/person/812559
4. mailto:3]mess20.bath.ac.uk
5. mailto:4]meelkot.zu.edu.eg
6. mailto:5]mahmoudelkot.gmail.com
7.
http://people.bath.ac.uk/mess20/
8.
http://www.bath.ac.uk/person/812559
9. mailto:mess20.bath.ac.uk
10. mailto:meelkot.zu.edu.eg
11. mailto:mahmoudelkot.gmail.com
12. mailto:AMBER.ambermd.org
13.
http://lists.ambermd.org/mailman/listinfo/amber
14.
http://people.bath.ac.uk/mess20/
15.
http://www.bath.ac.uk/person/812559
16. mailto:mess20.bath.ac.uk
17. mailto:meelkot.zu.edu.eg
18. mailto:mahmoudelkot.gmail.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 16 2011 - 12:30:03 PDT
