[gmx-users] Charmm36_lipids with gromacs

Peter C. Lai pcl at uab.edu
Sat Apr 7 03:53:15 CEST 2012

On 2012-04-06 08:04:56PM -0500, ffavela wrote:
> Dear gmx-users,
> I'm trying to do a minimization of a popc bilayer created with the VMD
> membrane builder plugin. I've followed some of the recommendations of
> Justin Lemkul to build the topology for my system, i.e., running pdb2gmx
> for one lipid (choosing the charmm36 force field I've downloaded from the
> gromacs page) and then include it as a .itp file in my system.top:
> #include "charmm36.ff/forcefield.itp"
> #include "popc.itp"
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> ; Include water topology
> #include "charmm36.ff/tips3p.itp"
> [ system ]
> ; name
> Pure POPC bilayer with 256 lipids and 4217 water molecules
> [ molecules ]
> ; name  number
> POPC    256
> SOL     4217
> When I run grommp to get the em.tpr (with the .mdp file that I got from
> the JL tutorials page for membrane) I get these warnings:
> WARNING 1 [file POPC255+WAT.top, line 31]:
>   38915 non-matching atom names
>   atom names from system.top will be used
>   atom names from system.gro will be ignored

What's calling POPC255+WAT.top?

Remember, discard the .top you get from pdb2gmx'ing the assembled PDB 
from VMD, since you're using the individual molecule .itp.

Check all your .top and .itp for spurious #include directives.

> WARNING 2 [file minim.mdp]:
>   The sum of the two largest charge group radii (14.681588) is larger than
>   rlist (1.200000)

Could be related to the POPC255+WAT.top issue (where I bet it has generated 
a single molecule topology).

But you may need to use -nochargegrp to pdb2gmx for charmm36 lipid still.

Here's a working popc.itp for use with charmm36:

> If I skip those warnings (what is wrong for sure) I get the em.tpr. If I
> run the mdrun I get this FATAL ERROR:
> Fatal error:
> There is no domain decomposition for 2 nodes that is compatible with the
> given box and a minimum cell size of 13.9221 nm
> Change the number of nodes or mdrun option -rdd
> Look in the log file for details on the domain decomposition

This looks related to the POPC255+WAT.top problem

Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|

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