[gmx-users] output coordinate file of ionic system

[Xavier Periole]

On Thu, 3 Jan 2008 17:20:35 +0800
  "renying" <yren at home.ipe.ac.cn> wrote:
> Dear GROMACS users,
>        I am performing a MD simulation  of protein in water using GROMOS96 
>force field. To neutralize the system, 10 NA+ are added in to neutralize the 
>system. Everything seems fine except the output coordinate file.
>        When computing on x nodes in parallel, the ions will be sorted into x 
> blocks for computation,and thus their coordinates are separated  in the 
>output file  *.gro . This really puzzles me because I have used the  -n *.ndx 
>option, so all the ions are expected to be continuous just as in the initial 
>*.gro file.  Can anyone give me some suggestions about this? Below are the 
>commands that I have used:
> 
> grompp  -np x -shuffle -sort -v -f pr.mdp -o pr.tpr -c after_em.gro   -p 
>*.top   -n *.ndx

The shuffle option is causing what you observe. If you want to keep
the order in the gro file you must remove the option.

> mpirun -np x mdrun -v -s pr  -o pr  -c after_pr   
> 
> 
>        Thanks a lot and happy new year to all  GROMACS users.  
> 
> 
> 
> 	
> 
> 	
> 
> Ying  Ren
> 2008-01-03
> 
> ----------------------------------------
> State Key Laboratory of Multi-phase Complex System
> Institute of Process Engineering (IPE)
> Chinese Academy of Sciences (CAS)
> P.O.Box 353, Beijing 100080, P.R. China
> Tel: +86-10-6255 5245 ext.1
>Fax: +86-10-6255 8065
> http://www.ipe.ac.cn/csms/
> ----------------------------------------
> 
> 　　　　　　　　　　

-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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