[gmx-users] Re: gromacs and pH description!

[Mark Abraham]

Florian Haberl wrote:

>>  1) how can i explaine "pH" into my system ( consisting protein & Na+ ions
>>) under gromacs? i'd like to reach to pH ~ 4.5 or 5 in my system.

What concentration of H+ ions are needed to get to these pH values? Can 
you do that in a system with 10^4 to 10^5 atoms? Even if you can, there 
are no MD water models that allow hydrogen atoms to dissociate freely, 
as happens in real water.

>> 2) is it
>>possible to introduce any kind of "free radicals" to a system consisting
>>protein and solvent?  i am trying to introduce some OH-  radicals into my
>>protein (which is related to aging phenomena) and seek every kind of
>>stractural changes that occurred on the protein structure after some ns
>>whithout any covalent bond breaking or formation as the first events in
>>every chemical reactions! how can i do that?

... by waiting about fifty years. To actually model bond breaking such 
as these radicals would be doing, you need to treat the electronic 
degrees of freedom, and reliable ab initio molecular dynamics on whole 
proteins will not be feasible for at least this long.

It does sound like you need to do some background reading on molecular 
simulations and their capabilities and limitations.

Mark