erikm at xray.bmc.uu.se
Sun May 20 21:35:19 CEST 2007
20 maj 2007 kl. 20.59 skrev David van der Spoel:
> Dmitriy Golubovsky wrote:
>> Dear Guru!
>> have you got any idea, on what how to calculate pH. for the system?
>> i'm solving a promblem of coil-globule transition for polymer.
>> do the topology for my structure(opls ff), do MD in water (spc).
>> get the statiscts. everything is ok.
>> the summary charge is equal to zero. no dissociation.
>> so the question is - how to calculate pH. or it's not possible?
>> if it is possible, than how to variate this pH in some range.
>> I allready try to use genion, but didn't get good results, on case
>> of very big dependence of the results from the initial
>> conformations of ions.
> How about computing the H3O+ concentration?
> It is close to impossible to simulate realistic pH with limited
> size systems. In practice your pH is always seven.
Depending on your specific application, CPHMD can be used to simulate
with constant pH. Unfortunately, CPHMD utilizes lambda-dynamics,
which is not yet implemented in gromacs. It should not be THAT hard
to implement yourself if you know a thing or two about MD and
programing in general.
> What do you mean with "no dissociation"?
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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