[gmx-users] MD production

[mihammad roos]

Hi everybody,


I’ve generated initial structure of my system by ambertoolsand convert the topology and coordinate files to Gromacs format by using parmEdto do the rest of simulation. Now, I’ve done the energy minimization andequilibration after that when I use the command “gmx_mpi grompp -f md.mdp -cnpt.gro -t npt.cpt -p gromacs.top -o md_0_1.tpr” for MD production I get thefollowing lines:


 
Ignoring obsolete mdp entry 'title'


 
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#

Setting the LD random seed to 4106683940

Generated 300 of the 300 non-bonded parameter combinations

Generating 1-4 interactions: fudge = 0.5

Generated 300 of the 300 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type 'system1'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'Na+'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'Cl-'

turning all bonds into constraints...

Excluding 3 bonded neighbours molecule type 'WAT'

turning all bonds into constraints...

Removing all charge groups because cutoff-scheme=Verlet

Analysing residue names:

There are:    20    Protein residues

There are:    27        Ion residues

There are: 13766     Water residues

Analysing Protein...

Analysing residues not classified as Protein/DNA/RNA/Waterand splitting into groups...

.

.

.

Fatal error:

41734 atoms are not part of any of the T-Coupling groups

For more information and tips for troubleshooting, pleasecheck the GROMACS

website at http://www.gromacs.org/Documentation/Errors

-------------------------------------------------------


 
Halting program gmx_mpi


 
gcq#27: "A Man Needs a Maid" (N. Young)


 
--------------------------------------------------------------------------

MPI_ABORT was invoked on rank 0 in communicatorMPI_COMM_WORLD 

with errorcode -1.


 
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPIprocesses.

You may or may not see output from other processes,depending on

exactly when Open MPI kills them.

--------------------------------------------------------------------------


My pdb file is consisted of 41734 atoms. I don’t know whatis wrong with my files. Can you please help me?


 
Thank you, Mohammad.