[gmx-users] How to neutralize net charge of protein and why

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 29 17:49:30 CEST 2009

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rituraj purohit wrote:
> Dear Friends,
> During first step of MD (pdb2gmx) I come to know that my protein having 
> net charge -42 e (it has two chain, A and B each having -21 e ).
> Why neutral system is preferable for further steps of MD & what kind of 
> problem encounter with charged system ?

There are theoretical reasons for not simulating a system with a net charge, but 
more intuitively, life does not exist at net charge.  For every positive, there 
is a negative somewhere.

> Should i have to add 21 Na+ to make it neutral, through "genion"?

No, you should add 42 Na+, since your system has a net -42e charge.


> Regards,
> Rituraj


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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