[gmx-users] Lipid Bilayer Simulations

Luca Mollica mollica.luca at hsr.it
Fri Sep 29 18:28:54 CEST 2006

Hi Mike!

 >      I am new to Gromacs, and I am working with
 > lipid bilayer simulations.
 > I am attempting to just run an energy minimization
 > on a lipid bilayer so I
 > can get a better feel for the program.  I have taken
 > the files dppc128.pdb,
 > dppc.itp, lipid.itp and example2.itp from Peter
 > Tieleman's website.
 > Because I could not use teh pdb2gmx command, I
 > started with the editconf
 > command and then the genbox command, both of which
 > seemed to run
 > successfully.  Then, I tried to do the preprocessing

actually, in this way you are more or less editing your files and adding some solvent molecules, nothing 
to do with FF & top/itp files related to lipid molecules ...

 > with the grompp
 > command, but I received the error; Fatal Error:
 > Found a second defaults
 > directive, file "lipid.itp".  When I removed
 > lipid.itp from the topology
 > file, I received the error; Fatal Error: Atomtype

Mm, ok ... I think you have two different solutions you can try:

1. Download from the website of GROMACS http://www.gromacs.org/contributed_by_users/task,cat_view/gid,37/
    a FF that is modified according to parameters describing lipids: I personally have inserted in my 	
    installation /usr/local/share/top (or whetheaver) directory these files and everything is working fine
    (both with 3.2 and 3.3 versions of GMX). In this way everything is included in the default FF and path
    in your machine. In case you do not have any access to your root directory and you are not the machine
    administrator, do not worry: insert all these untarred files in your working dir and everything will
    be fine! In this way you won'need any longer lipid.itp file for the used FF.

2. The second solution could simply be the usage of

	#include "lipid.itp"


	#include "dppc.itp"

    in the topology file as suggested in the other reply.

 > 'LC3' not found!  As I
 > said before, I am new to Gromacs, and I am not sure

    That's the point ! Actually GROMACS does not know who this guy is ....


Cheers and have nice MD on biomembranes


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