[gmx-users] error pull MD

[Mark Abraham]

wara boon wrote:
> Hello,
> 
> 
> I pull molecule into membrane by MD simulations but it error about
> 
> 
> processing topology...
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmx.itp
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxnb.itp
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/ffgmxbon.itp
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/ff_dum.itp
> 
> Generated 1284 of the 1485 non-bonded parameter combinations
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/spc.itp
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/ions.itp
> 
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_B'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_C'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_D'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_E'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_F'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_G'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_H'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_I'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_J'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_K'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_L'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_M'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_N'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_O'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_P'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_Q'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_R'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_S'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_T'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_U'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_V'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_W'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_X'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_Y'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein_Z'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'Protein'
> 
> turning all bonds into constraints...
> 
> Excluding 2 bonded neighbours molecule type 'SOL'
> 
> turning all bonds into constraints...
> 
> Excluding 3 bonded neighbours molecule type 'VIV'
> 
> turning all bonds into constraints...
> 
> processing coordinates...
> 
> double-checking input for internal consistency...
> 
> Velocities were taken from a Maxwell distribution at 325 K
> 
> renumbering atomtypes...
> 
> converting bonded parameters...
> 
> initialising group options...
> 
> processing index file...
> 
> Analysing residue names:
> 
> Opening library file /home/Ell/gromacMPI/share/gromacs/top/aminoacids.dat
> 
> There are:  3784      OTHER residues
> 
> There are:     0    PROTEIN residues
> 
> There are:     0        DNA residues
> 
> Analysing Other...
> 
> Pull group 0 'DPP' has 6400 atoms
> 
> Pull group 1 'VIV' has 32 atoms
> 
> Making dummy/rest group for Acceleration containing 17397 elements
> 
> Making dummy/rest group for Freeze containing 17397 elements
> 
> Making dummy/rest group for Energy Mon. containing 17397 elements
> 
> Making dummy/rest group for VCM containing 17397 elements
> 
> Number of degrees of freedom in T-Coupling group DPP is 12926.89
> 
> Number of degrees of freedom in T-Coupling group VIV is 62.99
> 
> Number of degrees of freedom in T-Coupling group SOL is 21928.12
> 
> Making dummy/rest group for User1 containing 17397 elements
> 
> Making dummy/rest group for User2 containing 17397 elements
> 
> Making dummy/rest group for XTC containing 17397 elements
> 
> Making dummy/rest group for Or. Res. Fit containing 17397 elements
> 
> Making dummy/rest group for QMMM containing 17397 elements
> 
> T-Coupling       has 3 element(s): DPP VIV SOL
> 
> Energy Mon.      has 1 element(s): rest
> 
> Acceleration     has 1 element(s): rest
> 
> Freeze           has 1 element(s): rest
> 
> User1            has 1 element(s): rest
> 
> User2            has 1 element(s): rest
> 
> VCM              has 1 element(s): rest
> 
> XTC              has 1 element(s): rest
> 
> Or. Res. Fit     has 1 element(s): rest
> 
> QMMM             has 1 element(s): rest
> 
> Checking consistency between energy and charge groups...
> 
> Calculating fourier grid dimensions for X Y Z
> 
> Using a fourier grid of 13x13x14, spacing 0.490 0.492 0.477
> 
> Pull group  natoms  pbc atom  distance at start     reference at t=0
> 
>        0      6400      3200
> 
>        1        32     17381   2.401                -99999.422
> 
> Estimate for the relative computational load of the PME mesh part: 0.49
> 
> This run will generate roughly 3 Mb of data
> 
> writing run input file...
> 
>  
> 
> There was 1 warning
> 
>  
> 
> -------------------------------------------------------
> 
> Program grompp_mpi, VERSION 4.0.2
> 
> Source code file: gmx_fatal.c, line: 481
> 
>  
> 
> Fatal error:
> 
> Too many warnings (1), grompp_mpi terminated.
> 
> If you are sure all warnings are harmless, use the -maxwarn option.
> 
> -------------------------------------------------------

There's no warning given in the partial output text you've supplied, so 
we can't help you diagnose. Also, you should update from 4.0.2, which is 
at least 6 months out of date.

Mark