[gmx-users] how to order atoms in GRO acording groups ?

[Anton Feenstra]

SemteX wrote:

> Hello gmx-users,
> 
> I have made MD with constrains and get *.gro file.
> 
> After grompp run i got warning about non-matching atoms, because after
> partial dynamics my atoms (molecules) of SOL and NA+ groups get
> disordered (differ from *.top file).
> 
> How to order my SOL and NA+ groups respectively ?

Did you use shuffling? If so, you must first unshuffle. Grompp will have 
written an index file (shuffle.ndx, or maybe deshuf.ndx) which you 
should use for that with editconf (e.g. 'editconf -n shuffle.ndx -f 
conf.gro -o deshuf.gro').


-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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