Please keep all GROMACS-related correspondence on the gmx-users list. I do not
advertise myself as a private tutor, nor do I claim to have all the answers.
You stand a much better chance of getting useful information by posting to the list.
The concept of pH in a simulation is a difficult one. You may find the
information here useful:
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation
In one sense, you can protonate residues according to how they would
predominantly exist at a given pH, but you can't really account for the effects
of proton transfer between residues. Protonation states can be assigned when
running pdb2gmx.
-Justin
Suguna wrote:
Dear Justin,
Iam S.Sugunadevi doing my Ph.D. in Korea. Iam very new to this field
(Molecular Dynamics). I got your ID from GROMACS mailing list.
I would like to do MD in different pH values. Kindly, could you guide
me, where to include that pH values and how?
Iam eagerly waiting for your responds.
Kindly help me.
Thanks in advance.
Regards
Sugunadevi.S
--
========================================
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
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
