[gmx-users] Reorder of residues and atoms

[Justin A. Lemkul]

xiaowu759 wrote:
> Dear gmxers,
> While performing EM using GMX, I find in the resullting gro file, 
> residues and atoms are reordered. Do this affect the simulation? Please 
> give me some hints. Thanks a lot!
> Before EM，gro file:
> 1  HmP   ......
> 2  HmP   ......
> .........
> 20 MmP .......
> 21 MmP ......
> .........
>  
> After EM, gro file:
> 20 Mmp ......
> 21 Mmp .....
> ......
> 1 HmP .....
> 2 HmP .......
> ......
>  

The order of the output is based on the order of the input molecules listed in 
the [molecules] directive of the .top.  If you received warnings from grompp 
that there were mismatching names in the topology, then the wrong parameters may 
have been applied to the molecules in your system.  The order of the [molecules] 
directive must match that of the coordinate file.

-Justin

>  
> ------------------
> /Department of Chemistry and Materials Science///
> /Hunan University of Humanities, Science and Technology, /
> /Loudi 417000, the People's Republic of China (P.R. China)/
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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