Sathish wrote:
Dear all,
How to run simulation in different PH?
Kindly help to fix this problem. Thanks in advance...
The concept of "pH" is ill-defined for an MD system, the reasons for which have
been discussed at length in recent days even (hint: please check the archive
before posting). Issues arise with the inability to change protonation,
inadequate hydronium parameters, inability to model systems of sufficient size
to even achieve a proper pH, and the list goes on.
The best you might hope for is not a change in "pH" (per strict definition), but
rather changing the protonation state of titratable groups in your system
according to pKa.
-Justin
--
========================================
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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