[gmx-users] How can I generate a Input *.gro file of coarse grain model?

[s4026869 at student.uq.edu.au]

Hi xuji,

I do not believe the scripts provided on the site deal with water.  
That is, unfortunately, you cannot take and equilibrated atomistic  
system and convert directly to the CG representation.

What you will have to do is go to the "test/model" system page and  
download the pure water system. You can then use this as an input to  
genbox program.

Cheers

Mitch



Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

> There are scripts provided on the MARTINI site to generate the
> necessary structure files, and the topology, IIRC.
>
> -Justin
>
> xuji wrote:
>> Dear all gromacs users:
>>
>> I am trying to use the MARTINI CG force field from Marrink et al.   
>> in my simulation. But I don't konw how to generate the input *.gro   
>> files.
>> When I use all-atom model, in gromacs I can use "genbox" "editconf"  
>>  et al to generate
>> the input *.gro files. For example, I can use "genbox -cs -box 10   
>> 10 10 -o waterbox.gro"
>> to generate pure water box. But if I only have the files downloaded  
>>  from "http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html" ,  
>> and  I use a *.top file which contains:
>>
>> #include "martini_v2.0.itp"
>> #include "martini_v2.0_lipids.itp"
>>
>> [ system ]
>> DPPC BILAYER [ molecules ]
>> DPPC 128
>> W 2000
>>
>> Can I generate a *.gro file according to this topology file using   
>> Gromacs' tools?
>> If can, how do it?
>>
>> Appreciate any help in advance!
>>
>>
>>
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www   
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php