[gmx-users] Newbie question

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 23 15:47:16 CEST 2008

Andres Rojas Guerrero wrote:
> Hi, I'm newbie in Gromacs and MD, I'm reading the Tsjerk excellent 
> tutorial. In the part of Addition of Ions, Tsjerk said that we need to 
> edit the topology file and the decrease the number of solvent 
> molecules, and add a line specifying the number Na+ and Cl-. How can I 
> do this?  Let me explain, in the topology file I have:
>  [ molecules ]
> 10565 ; Compound        #mols
> 10566 Protein_A           1
> 10567 SOL               198
> 10568 SOL             10277

I'm guessing the numbers in the left-most column (10565 - 10568) are 
superfluous line indicators, otherwise they will be problematic :-)

What genion does is replace water molecules with the ions you 
specified.  So, for each ion added, subtract one water (SOL) molecule.

You can also merge the SOL definitions into one, there is no reason for 
crystal waters(?) to be distinct from any others.  You will end up with 
a [molecules] section that looks like:

Protein_A      1
SOL            10475 - x - y
NA+            x
CL-            y

(substituting, of course, the appropriate names for your ions).


> What number I need to change? and what it's the fomat to add the ions 
> Na+ and Cl- to topology file?
> Thank you very much.
> Andres.
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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