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

[Mark Abraham]

On Wed, Apr 16, 2014 at 12:27 PM, Valentina <valentina.erastova at durham.ac.uk
> wrote:

> 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:
>

Yes, the coordinate file must match the ordering implied by the [molecules]
section. I've not tried it, but I expect that matching that section to the
contents of the coordinate file will work. You can probably do the
solvation stage last of all to make life easier.

Mark


>
> 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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