[gmx-users] genconf of box of a few types of molecules

[Valentina]

Hello,
It would be good to know, if I am missing something out here. Thank you!

I have a set up box of a few components: a material layer (MIN), peptide
(ASP) and water (SOL).
system.gro file it looks like this:

1MIN ...
2MIN ...
3ASP ...
4ASP ...
5SOL ...
6SOL ... 

system.top
... 
[ molecules ]
MIN 2
ASP 2
SOL 2

I want to scale the system up, so I use genconf. genconf just stacks the
system, so say I double it and then systemx2.gro file looks like this:

1MIN ...
2MIN ...
3ASP ...
4ASP ...
5SOL ...
6SOL ... 
7MIN ...
8MIN ...
9ASP ...
10ASP ...
11SOL ...
12SOL ... 

In topology I double number of molecules, getting this 
systemx2.top
...
[ molecules ]
MIN 4
ASP 4
SOL 4

BUT gromacs doesn't seem to like this approach, it wants to have things
ordered in the .gro file:

1MIN ...
2MIN ...
3MIN ...
4MIN ...
5ASP ...
6ASP ... 
7ASP ...
8ASP ...
9SOL ...
10SOL ...
11SOL ...
12SOL ... 

the genbox option -sort and -renumber are not for this purpose

Is there a trick within gromacs to do it, or do I have to master sed/awk :(
?

Thank you,
V



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