[gmx-users] Genbox problem ...

Kedar Potdar kedar.potdar at gmail.com
Tue May 29 14:45:25 CEST 2007

Hi friends,


I have compiled Gromacs on native windows. The first two program in demo
script (perl implementation of script "demo") work fine but genbox displays
following output 


Reading solute configuration

Glycine aRginine prOline Methionine Alanine Cystine Serine

Containing 145 atoms in 13 residues

Initialising van der waals distances...

Reading solvent configuration

"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"

solvent configuration contains 648 atoms in 216 residues


Initialising van der waals distances...

Will generate new solvent configuration of 2x2x2 boxes

Generating configuration

Sorting configuration

Found 1 molecule type:

    SOL (   3 atoms):  1728 residues

Calculating Overlap...

box_margin = 0.315

Removed 2895 atoms that were outside the box

Succesfully made neighbourlist

nri = 11448, nrj = 456822

Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms.

Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms.

Added 488 molecules

Generated solvent containing 1464 atoms in 488 residues

Writing generated configuration to cpeptide_b4em.gro

Glycine aRginine prOline Methionine Alanine Cystine Serine


Output configuration contains 1609 atoms in 501 residues

Volume                 :     17.1176 (nm^3)

Density                :     1002.99 (g/l)

Number of SOL molecules:    488


Processing topology


Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1#


Cpeptide.top file is of zero bytes now. and all further programs in the test
fail after this.


Has anybody faced such problem before? What is remedy for this problem?


With warm regards,




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