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
--
========================================
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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