[gmx-users] proton proton exchange and constant pH simulations.

[Miguel Machuqueiro]

On 27-01-2011 11:29, Mark Abraham wrote:
> On 27/01/2011 9:44 PM, Olga Ivchenko wrote:
>> Dear gromacs users,
>>
>> I want to ask if is it possible to amke proton proton exchange
>> simulations by now and constant pH simulations in new versions of Gromacs.
> Not sure what you mean, but probably not. See recent publications from
> Lindahl group for what is possible.
>
> Mark

Hi all,

Constant-pH MD simulations using an older version of gromacs (v. 3.2.1) 
is possible:

http://dx.doi.org/10.1021/jp056456q
http://dx.doi.org/10.1529/biophysj.106.092445
http://dx.doi.org/10.1002/prot.21923
http://dx.doi.org/10.1021/ja808463e
http://dx.doi.org/10.1021/jp104753t

Unfortunately, newer versions (v. 4.x.x) do not allow the use of Freeze 
Groups in NPT simulations, which is essential for the method to work. In 
case this is "solved" in future releases, we will port the method to new 
and faster gromacs versions.

Regards,

-- 
============================================
Miguel Machuqueiro
Department of Chemistry and Biochemistry
Faculty of Sciences, University of Lisbon
Campo Grande, Edifício C8 (sala 8.5.47)
1749-016 Lisboa, Portugal
Tel.  : +351 217500112 (int.ext.28547)
Mobile: +351 967562285
E-mail: machuque at fc.ul.pt
www1: http://webpages.fc.ul.pt/~mamachuqueiro
www2: http://intheochem.fc.ul.pt
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