[gmx-users] genbox -nmol, atoms removed

[Justin Lemkul]

On 12/31/12 9:41 PM, Xu Dong Huang wrote:
> 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?
>

You're doing too much at once.  Run the -ci -nmol options in one step, then 
solvate with -cs.  You can also specify exact starting positions for each 
individual molecule with editconf -center, which may be a more foolproof 
solution for complex systems.  As I recall, -ci has issues with multi-residue 
molecules, but perhaps that's an old issue and is no longer relevant.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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