[gmx-users] simulation at particular pH

Arthur Roberts aroberts99163 at yahoo.com
Tue Aug 8 21:16:19 CEST 2006

Hi, Luisa,

I would first calculate the number of protons (H+)
that you would find your water box. Then I would use
the command genion to generate that number of H+'s
that corresponds to the pH.  Then I would use grompp
to find out what the final charge is.  If it is still
negative, I would add NA+.  If it is positive, I would
add CL-.  This should approximate the pH.  Although
there is one problem, ionizable residues.  You will
need to set those manually.  I am not sure, if you can
use the morse potential on specific residues instead
of harmonic potential to make a residue ionizable.  I
hope this helps.

Best wishes,
Art Roberts
University of Washington
Department of Medicinal Chemistry

--- luisa pugliese
<luisa.pugliese at safan-bioinformatics.it> wrote:

> Hello to everybody,
>    I am new to this mailing list and I am writing
> because I wonder if anybody knows how can I set up
> the pH of the system in gramacs.
> Thank you to everybody
> Luisa
> =============================
> Luisa Pugliese, Ph.D.
> luisa.pugliese at safan-bioinformatics.it
> Corso Tazzoli 215/13 -10137 Torino - ITALY
> tel +39 011 3026230
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