Mark, I've checked only density value
with 500 molecules Ccl4 I have density that is twisely less that I need ( in accordance to the literature ). Also I've checked my box visually and found that the box is not properly tightly packed so I dont know why genbox didnt add some extra mollecules :( In other words I wounder to know if there is any way to add some extra molecules to the pre defined box to make my system more tighly packed ( to short distance between existing molecules and place new ones in the new space ) ? James 2012/2/14 Mark Abraham <mark.abra...@anu.edu.au> > On 14/02/2012 4:57 PM, James Starlight wrote: > >> Justin, >> >> Firstly I've created the box of desired size with only 500 molecules ( I >> need 1000) >> >> Than I've tried to add extra 200 molecules by means of Genbox >> >> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro >> >> but no molecules have been added >> Added 0 molecules (out of 200 requested) of Cl4 >> > > ... then there are no gaps large enough to insert your molecules. Either > make gaps, or check out genbox -h for advice on defining the radii. > > > >> also I've tried >> >> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro >> > > Two -cp options is not what you want, and -nmol probably only works with > -ci. > > > >> but system were crashed with message >> >> Reading solute configuration >> God Rules Over Mankind, Animals, Cosmos and Such >> Containing 2500 atoms in 500 residues >> Initialising van der waals distances... >> >> WARNING: masses and atomic (Van der Waals) radii will be determined >> based on residue and atom names. These numbers can deviate >> from the correct mass and radius of the atom type. >> >> Reading solvent configuration >> "God Rules Over Mankind, Animals, Cosmos and Such" >> solvent configuration contains 5 atoms in 1 residues >> >> >> Is there any ways to add extra mollecules to the pre defined box ? >> > > Yes - but there has to be room for them. > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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