[gmx-users] output coordinate file of ionic system

[renying]

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   
 

        Thanks a lot and happy new year to all  GROMACS users.  



	

	

Ying  Ren
2008-01-03

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State Key Laboratory of Multi-phase Complex System
Institute of Process Engineering (IPE)
Chinese Academy of Sciences (CAS)
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