leila karami wrote:
Hi
How I exert my favorite PH in simulation of pr-dna interaction in mdp
file? And also special concentration of some salts.
The concept of pH is not one that can be easily defined in a normal MD
simulation. Please see the extensive discussion here:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
You can, however, assign protonation states to your various amino acids when
running pdb2gmx.
To alter salt concentration, please see genion -conc.
-Justin
Any help will highly appreciated!
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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