[gmx-users] pH and Temperature

Lucio Montero lucioric at ibt.unam.mx
Fri Jan 17 17:52:38 CET 2014

El 13/01/14 15:17, Mostafa Javaheri escribió:
> ​Dear Justin
> I want to
> simulate a protein in human’s body temperature (37° Celsius,
> 98.6° Fahrenheit),
> Is
>   this OK to set ref-t: 310 in nvt.mdp file or I have to start from lower
>   temperature
> e.g. 300, 200, 100 then increasing it step by step till reaching the
> desired
> temperature? Will the simulation be OK if I start from 310 K? Many
> researchers prefer 300 k, is this the optimum temperature for all
> GROMACS simulation?
> What is the default pH value for mdrun and could I change it?
> Sincerely
> M.Javaheri
Mdrun doesn't know of pH as a numerical value, the only way to simulate 
the pH is to explicitly add the hydrogen or hydroxyl ions, that at 
neutral pH are too little quantity of ions. Which one should do is to 
equilibrate the charges with counterions, and if you should have a 
certain ionic stength, you may add more salt ions.
Best regards

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