[gmx-users] .gro File manipulation

[Mark Abraham]

I would equilibrate membrane only first, particularly if I was going to
reuse it a few times, but there may not be much in it!

Mark
On Feb 13, 2014 12:55 PM, "Andres Ortega Guerrero" <og_andres15 at hotmail.com>
wrote:

> Hi mark thanks for the help, I was wondering , if you mean , the entire
> structure with when membrane protein , and the whole system, or to do one
> equilibration process first with the membrane ?
>
> Thanks
>
> Andrés Ortega
> Ing. Electrónica
> Universidad del Valle
>
> El 13/02/2014, a las 6:20, "Mark Abraham" <mark.j.abraham at gmail.com>
> escribió:
>
> > Hi,
> >
> > I think you want genbox -cs membrane -box x y z (and a lot of
> > equilibration).
> >
> > Mark
> >
> >
> > On Thu, Feb 13, 2014 at 6:13 AM, Andres Ortega <og_andres15 at hotmail.com
> >wrote:
> >
> >> Dear Gromacs Users,
> >>
> >> I hava a membrane channel in a .gro file, but the -n and -c terminal are
> >> bigger, i mean the channel box is bigger( in x and y) than the membrane
> >> (512
> >> POPC) ,
> >> my 512 POPC is created using genconf with a 128POPC
> >> so i create a 1152 POPC with genconf nbox 3 3 1 , but there are to much
> >> POPC
> >> molecules,
> >> is there a tool in gromacs that i can select the box size and just that
> >> POPC
> >> molecules in that box instead of using the entire membrane,
> >>
> >> or i have to chech the 128POPC, and delete molecule, and then prepare a
> >> more
> >> adecuate membrane.gro with genconf ?
> >>
> >> I would appreciate any help or advice
> >>
> >> Andres
> >>
> >> --
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