[gmx-users] output coordinate file of ionic system

[Jochen Hub]

renying 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
> mpirun -np x mdrun -v -s pr  -o pr  -c after_pr   
>   
When using -shuffle, grompp writes an index file deshuf.ndx. You can use
deshuf.ndx to "deshuffle" the coordinate output (xtc, trr, gro) of mdrun
using trjconv or editconf:

trjconv -n deshuf.ndx -f traj.xtc -o deshuffled.xtc
editconf -f confout.gro -n deshuf.ndx -o deshuffled-confout.gro

Good luck,
Jochen

>  
>
>         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)
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-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************