[gmx-users] calculate potential in the box contain ions

Justin A. Lemkul jalemkul at vt.edu
Sun Jul 31 06:05:27 CEST 2011

Please keep the discussion on the list; I'm not a private tutor.

Saeid Akbarshahi wrote:
> Dear Justin
> I have simulated this system with this structure and files.Could you 
> tell me, is my structure correct?

I have no clue what is in your system, what settings were used for the 
simulation, or anything else so I cannot make any assessment whatsoever.

> I am a novice user.

It is in your best interest to do lots of homework before running a simulation 
and hoping it's right.  Ask yourself: what protocols have others used?  What 
have they analyzed?  Why have they done these things?  Unless you can answer all 
of these questions and understand the logic behind the choices made, you're not 
ready to do simulations if you rely on keeping your fingers crossed, hoping to 
have someone check your work for you.  There is a steep learning curve for doing 
MD simulations properly, but doing the proper preparation now will save you tons 
of time (and wasted data) later on.



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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