[gmx-users] Gromacs 4 with mpi interface

[Justin A. Lemkul]

 From genion -h:

"genion replaces solvent molecules by monoatomic ions at the position of the
first atoms with the most favorable electrostatic potential or at random."

That would explain how genion works, and what you must do to update the topology 
correctly.  If you have added 2 NA+, then you have also removed 2 SOL.

-Justin

Chitrita Dutta Roy wrote:
> What exactly Do we need to change in the topology file suppose if we add 
> 2 NA+ ions in the system..???
> 
> On Thu, Dec 18, 2008 at 1:45 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Chitrita Dutta Roy wrote:
> 
>         Can anyone give me a detailed notes on how to install gromacs 4
>         with mpi feature..I am using Intel Q9300 and fedora 10.It's very
>         urgent as i am new to using gromacs plz give me as detailed note
>         as possible..
> 
> 
>     Installation instructions are on the Gromacs webpage and the wiki
>     site (including a heading called "Using MPI").
> 
> 
>         And after adding some ions using genion when i try to run grompp
>         again before final mdrun i get some error telling mismatches in
>         .top and .gro file in some atoms although i have changed the top
>         files as normally we should adding the ions and changing the
>         total number of solvents accordingly..Why is it happening Can
>         anybody help..plzz??
> 
> 
>     Then you haven't updated your topology correctly.  Without seeing
>     your command line and the output, it's hard to say much more.  The
>     wiki site (again) is your friend here.
> 
>     -Justin
> 
> 
>         Thanks.
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================