vivek sharma wrote:
hi Justin,
Thanks for your reply...
I am interested in looking for the stability of the docked pose, by
applying some temperature variation in the molecule.
If I am applying temperature variation then should I use pressure
coupling simultaneously.
Well that's going to depend on how much you're varying the temperature. I have
a colleague who has done some thermal stability simulations upwards of 600K and
the NPT algorithm breaks down (using AMBER). I don't know if that's true of the
Gromacs code as well.
Can you suggest some tutorial for such attempts.....
Well, I don't know about tutorials, but (again depending on how much you're
varying the temperature) some of the literature regarding thermal stability of
proteins over wide temperature ranges might be of interest.
-Justin
With Thanks,
Vivek
2008/11/10 Justin A. Lemkul <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>
vivek sharma wrote:
Hi There,
I am running MDS over the docked poses to check the stability of
the docked poses using gromacs.
I have few doubts about selecting parameters for the same, If
anybody have tried such thing earlier, please suggest me for the
same.
Should I keep pressure coupling over the simulation ?
Sure; life exists at NPT, so it is commonly used in routine protein
simulations.
For how long should I run the simulation for such purpose ?
That's up to you :) You should run the simulations as long as you
feel necessary to achieve stability. I know that's vague, but there
really is no single correct answer to this question in the MD field.
If there is, I'd love for someone to tell me, too...;)
-Justin
Waiting for suggestions.
With Thanks,
Vivek
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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