On Sat, 15 Dec 2007 21:58:37 -0500
"Justin A. Lemkul" <[EMAIL PROTECTED]> wrote:
Quoting pragya chohan <[EMAIL PROTECTED]>:
Dear Users
I have a system in of protein with in bound chlorine ion. I also added Na
ion
to the system to neutralize charge on system. I have to couple the system to
water bath. can i couple protein chlorine and Na together and solvent
separately? or should i couple protein and chlorine together and solvent and
na together?
You could do either. Try make_ndx -h. But generally, when I simulate a
protein in water and ions, I simply couple the whole system to the same
bath.
You do not want to couple the whole system to one bath. Due to the
exchange of kinetic energy between water and protein you'll end up
with a frozen protein and warm water.
This is simply due to the different behavior of the water and the
protein relative to the integration of the equation of motion.
Integration errors are much more on the solvent, which warms it up;
the use of constraints removes kinetics energy on the direction of
the bonds and proportionally more on the protein, which cools down.
Thus, even if these effects are very small they add up to make the
solvent warmer than the protein cooler. Coupling the whole system
to one bath would thus generate energy exchange to compensate the
temperature difference. On top of this the bath would tend to decrease
the temperature of the whole system although only the solvent is
getting warmer. The protein ends up frozen.
I would suggest to Justin to check the temperature of your protein and
your solvent separately. You should see this effect.
The suggestion of Mark to couple the ion to the part of the system it
belongs to (protein or solvent) is certainly the best.
See here:
http://wiki.gromacs.org/index.php/Thermostats
I the later case -n option would take in 2 index files. then what should I
do?
Specify both groups within the same index file. Again, make_ndx -h. Type
'help' for some examples.
-Justin
Thanks in advance
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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-----------------------------------------------------
XAvier Periole - PhD
NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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