On 10/18/12 12:06 PM, Arman M. Soufiani wrote:
Dear all friends,
I wonder why we should impose POSRES on the protein in the system while
running NVT?! Shall we do so even for the system containing a short
peptide?!
Velocity generation causes atoms to move randomly, which can impart nasty forces
on your solute. Restraining the solute helps preserve its structural integrity.
What if I let the peptide, SOL+ions and my system's synthetic polymer apply
T-coupling individually?
That depends on the size of each component.
http://www.gromacs.org/Documentation/Terminology/Thermostats
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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