parthi...@ncbs.res.in wrote:
Hi
can any one could help me in, How to include the pH for doing MD studies.
My interest is to include the pH at the initial time duration and to
change the pH from 4 to 7 during the course of simulation.
is there any possibility in performing such work in gromacs.
No. Changing the pH over the course of a simulation would lead to changing the
protonation state of titratable residues and is therefore not possible in MD,
since you would be breaking and forming bonds. Running independent simulations
that represent different pH values might be more reasonable, by protonating
these residues appropriately when running pdb2gmx and defining the topology that
would correspond to a given pH value.
-Justin
Thanks in advance
Parthiban
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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