[gmx-users] pH

Ilya Chorny ichorny at maxwell.compbio.ucsf.edu
Mon Mar 22 05:30:01 CET 2004

The number of protons present at ph = 7.0 is
10^-7M. Thats 10^-7 moles of protons in about
55 moles of water. 1 proton in 10^9 water molecules. Most
simulations are on the order of 10^3-10^4

The pH for most relevant pH ranges is determined
by the protonation state of the molecules in the water and not by
the water.


-----Original Message-----
From: gmx-users-admin at gromacs.org [mailto:gmx-users-admin at gromacs.org]On
Behalf Of Dallas Warren
Sent: Sunday, March 21, 2004 1:34 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pH

>What pH are the simulations in GROMACS carried out at?

You set that yourself.

>Is here anyway to change that pH?

Change the protonation of the species present in the simulation.

There is a thread on the emailing list back from about 2 months ago or so,
that covers this in some detail.

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
When the only tool you own is a hammer, every problem begins to resemble a

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