[gmx-users] pH

Erik Marklund erik.marklund at chem.ox.ac.uk
Mon Jun 29 10:17:41 CEST 2015


Dear Atila,

With the official release, you set the protonation state of titratable groups according to what you expect based on their pKa. This can be done interactively with pdb2gmx. Note that this yields static protonation states, as bonds are not broken during the simulation. Also note that the pKa of a group might be shifted somewhat by the environment, so this is not entirely straightforward.

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

> On 29 Jun 2015, at 07:22, Atila Petrosian <atila.petrosian at gmail.com> wrote:
> 
> Dear Gromacs users,
> 
> I read some papers in which  MD simulation was done under the pH other than
> 7.
> 
> How to do this using gromacs package?
> 
> Thanks in advance,
> Atila
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