[gmx-users] PH of system

[jkrieger at mrc-lmb.cam.ac.uk]

There is documentation on this at
http://www.gromacs.org/Documentation/How-tos/Constant_pH_Simulation but
the link to the mailing list there is out of date.

Also what about the method of Lee et al., J. Chem. Theory Comput., 2014 (
http://pubs.acs.org/doi/full/10.1021/ct500175m )? I guess once Enveloping
Distribution Sampling is implemented (Michael Shirts was planning this for
5.2 in Nov 2014:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2014-November/008100.html
) then protonation with HREx and EDS could follow. Not being at all
involving in any developing myself I don't know how feasible this is or
how long it would take.

Best wishes
James

>
>
> On 12/20/15 11:36 PM, Sana Saeed wrote:
>> hi gmx usershow would i know the PH of the system, and how to manage the
>> value of PH, WHAT should i CHANGE to simulate a system at PH =2
>
> Check the archive; this comes up all the time.  Short answer: you can't
> really
> claim that any constant topology system without hydronium actually has a
> pH
> value.  What you can say is that you have protonated all relevant
> molecules at
> their predominant form at a given pH.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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