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

[Tsjerk Wassenaar]

Hi,

Alternatively, you can write a file single.itp, containing

MIN 2
ASP 2
SOL 2

And in the .top file have:

[ molecules ]
#include "single.itp"
#include "single.itp"


Cheers,

Tsjerk



On Wed, Apr 16, 2014 at 12:42 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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
> >
> >
> >
> > --
> > View this message in context:
> >
> http://gromacs.5086.x6.nabble.com/genconf-of-box-of-a-few-types-of-molecules-tp5015876.html
> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> > --
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-- 
Tsjerk A. Wassenaar, Ph.D.