[gmx-users] genbox -nmol, atoms removed

[Xu Dong Huang]

Thank you very much. I got it sorted out by following your advice. 


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

On Dec 31, 2012, at 10:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 
> 
> 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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