[gmx-users] Newbie question

Marcus Kubitzki mkubitz at gwdg.de
Mon Jun 23 15:48:27 CEST 2008

Hi Andres,

in total you have 10475 (198+10277) SOL molecules, so you can condense
the two SOL lines into one. Suppose you add 20 NA+ and 20 CL-, you
subtract 40 SOL molecules from the system and add 40 ions in total. So
you write:

[ molecules ]
; Compound        #mols
Protein_A           1
SOL             10435
NA+                20
CL-                20

There are now 40 SOL molecules less (10475-30=10435) and the ions are
added. Don't forget to add an #include "ions.itp" under
"Include generic topology for ions"


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
> 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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Dr. Marcus Kubitzki
Max Planck Institute for Biophysical Chemistry
Computational Biomolecular Dynamics Group
Am Fassberg 11
D-37077 Göttingen
phone: ++49-551-2012312
fax: ++49-551-2012302
Email: mkubitz[at]gwdg.de
www: http://www.mpibpc.mpg.de/groups/de_groot/

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