[gmx-users] Charmm36_lipids with gromacs

Justin A. Lemkul jalemkul at vt.edu
Sat Apr 7 03:31:41 CEST 2012

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

In this case, the listing of your [molecules] directive does not match that of 
your coordinate file.  It needs to.

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

I suspect your molecules are broken across periodic boundaries, as suggested here:


> 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 is a consequence of the above error.  Even if your system ran, the mismatch 
between coordinates and topology will map the wrong parameters to each species 
and thus the simulation will crash anyway due to physical instability.


> Any comment will be appreciated. Thanks in Advance.
> Cheers,
> Fernando. 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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