Dear Carlos,
Thanks for your comments. I am actually familiar with conventional/standard
MD parameters in Amber (guided by the tutorials and some personal
communications). In principle, I like to simulate the HIV PR flap
opening-closure process but I was not sure about the
keywords/flag/parameters ( as you mention below ntt=3 and gamma_ln value)
that best specify the viscosity. I came across one of your publications in
PNAS which address the issue so I though that you are the best I can contact
for help..
Thanks any way
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
Email:
[3]mess20.bath.ac.uk
[4]meelkot.zu.edu.eg
On 3/9/11 2:19 PM, Carlos Simmerling wrote:
definitely check out the tutorials on the amber web site if you have not
already.
you'll want to use one of the GB models for the simulation- there are
several, and the pro/con have been fairly well discussed in the literature.
which one is "best" depends on what you are simulating.
the viscosity is controlled with Langevin dynamics (ntt=3 in amber) and
gamma_ln (lower is less). There is a paper a while back from Pande showing
folding rates as a function of viscosity.
I suggest doing the tutorials and coming back with specific questions once
you're up and running.
good luck!
On Tue, Mar 8, 2011 at 3:28 PM, Mahmoud Soliman [5]<mess20.bath.ac.uk> wrote:
Hi guys!
I need to simulate some big conformational changes in some protein
structure
and I came across a paper reporting that continuum solvation with low
solvent viscosity has proved good ensemble. Do you guys have any previous
experience with such MD conditions and what keywords I can use in Amber
script....
Thanks in advance
Best wishes
mahmoud
--
**************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[1][6]
http://people.bath.ac.uk/mess20/
[2][7]
http://www.bath.ac.uk/person/812559
Email:
[[8]3]mess20.bath.ac.uk
[[9]4]meelkot.zu.edu.eg
References
1. [10]
http://people.bath.ac.uk/mess20/
2. [11]
http://www.bath.ac.uk/person/812559
3. [12]mailto:mess20.bath.ac.uk
4. [13]mailto:meelkot.zu.edu.eg
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[15]
http://lists.ambermd.org/mailman/listinfo/amber
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[17]
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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:mess20.bath.ac.uk
6.
http://people.bath.ac.uk/mess20/
7.
http://www.bath.ac.uk/person/812559
8. mailto:3]mess20.bath.ac.uk
9. mailto:4]meelkot.zu.edu.eg
10.
http://people.bath.ac.uk/mess20/
11.
http://www.bath.ac.uk/person/812559
12. mailto:mess20.bath.ac.uk
13. mailto:meelkot.zu.edu.eg
14. mailto:AMBER.ambermd.org
15.
http://lists.ambermd.org/mailman/listinfo/amber
16. mailto:AMBER.ambermd.org
17.
http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 09 2011 - 06:30:05 PST
