[gmx-users] genbox -nmol, atoms removed

Xu Dong Huang xudongh at eden.rutgers.edu
Tue Jan 1 03:41:48 CET 2013

Dear Advanced Gromacs users,

I'm trying to generate a solvated system with >1 solute (In my case 3). I do genbox -cp polymer.gro -nmol 2 -ci polymer.gro -cs water.gro -o polymer_solv.gro -p polymer.top 

My polymer molecule contains 201 atoms. box size 45x45x45

and it generates a system with the following messages: 

Found 1 molecule type:
      W (   1 atoms): 4259200 residues
Calculating Overlap...
box_margin = 0.315
Removed 0 atoms that were outside the box
Neighborsearching with a cut-off of 0.315
Table routines are used for coulomb: FALSE
Table routines are used for vdw:     FALSE
Cut-off's:   NS: 0.315   Coulomb: 0.315   LJ: 0.315
System total charge: 0.000
Grid: 254 x 254 x 254 cells
Successfully made neighbourlist
nri = 1851, nrj = 1983
Checking Protein-Solvent overlap: tested 867 pairs, removed 277 atoms.
Checking Solvent-Solvent overlap: tested 1100 pairs, removed 0 atoms.
Added 4258923 molecules
Generated solvent containing 4258923 atoms in 4258923 residues
Writing generated configuration to star_solv.gro
star polymer

Output configuration contains 4259727 atoms in 4258971 residues
Volume                 :      512000 (nm^3)
Density                :     2539.37 (g/l)
Number of SOL molecules:      0   

**My problem is, the output configuration contains unequal amount of atoms and residues, and when I do the subtraction, the difference is the exact amount of atom of my original polymer molecule. (I'm assuming genbox removed my molecule out of the box)
-How can I prevent that from happening? So that I can put as many additional polymer in the solvated system as I want? 


Xu Dong Huang
Chemical & Biochemical Engineering
Rutgers School of Engineering 
xudongh at eden.rutgers.edu 

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