[gmx-users] MD production

[Justin Lemkul]

On 12/16/15 8:47 AM, mihammad roos wrote:
> 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?
>
>

The error is obvious:

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

Set tc-grps appropriately.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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