[gmx-users] .gro File manipulation

[Andres Ortega Guerrero]

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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