[gmx-users] Charmm36_lipids with gromacs

ffavela ffavela at fis.cinvestav.mx
Sat Apr 7 03:04:56 CEST 2012

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"

; 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

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

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

Any comment will be appreciated. Thanks in Advance.

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