[gmx-users] pH and Temperature

Mostafa Javaheri m.javaheri at gu.ac.ir
Mon Jan 13 22:22:40 CET 2014

​Dear Justin

I want to
simulate a protein in human’s body temperature (37° Celsius,
98.6° Fahrenheit),
 this OK to set ref-t: 310 in nvt.mdp file or I have to start from lower
e.g. 300, 200, 100 then increasing it step by step till reaching the 
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? 



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