Thank you very much. I got it sorted out by following your advice.
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 10:23 PM, Justin Lemkul <jalem...@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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists