[gmx-users] error pull MD

[wara boon]

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.

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


Have a nice dayWara

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090618/a42d825b/attachment.html>