Telling the truth I don't know how these values are calculated and why genbox needs them. Maybe somebody in the list can advise...
> Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 > System total charge: 0.000 On Thu, Aug 13, 2009 at 9:23 PM, Jamie Seyed<[email protected]> wrote: > Hi Vitaly, > This is after runing genbox: > ----------------------------------- > opening library file > /home/seyedyazdij/gromacs-4.0.5/share/top/aminoacids.dat > WARNING: masses will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file > /home/seyedyazdij/gromacs-4.0.5/share/top/atommass.dat > Entries in atommass.dat: 178 > WARNING: vdwradii will be determined based on residue and atom names, > this can deviate from the real mass of the atom type > Opening library file > /home/seyedyazdij/gromacs-4.0.5/share/top/vdwradii.dat > Entries in vdwradii.dat: 28 > Opening library file > /home/seyedyazdij/gromacs-4.0.5/share/top/dgsolv.dat > Entries in dgsolv.dat: 7 > Opening library file > /home/seyedyazdij/gromacs-4.0.5/share/top/electroneg.dat > Entries in electroneg.dat: 71 > Opening library file > /home/seyedyazdij/gromacs-4.0.5/share/top/elements.dat > Entries in elements.dat: 218 > Reading solute configuration > Fullereno in vacuum > Containing 60 atoms in 1 residues > Initialising van der waals distances... > Reading solvent configuration > > "216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984" > solvent configuration contains 648 atoms in 216 residues > > Initialising van der waals distances... > Will generate new solvent configuration of 1x1x1 boxes > Generating configuration > Sorting configuration > Found 1 molecule type: > SOL ( 3 atoms): 216 residues > Calculating Overlap... > box_margin = 0.315 > Removed 528 atoms that were outside the box > Neighborsearching with a cut-off of 0.45 > Table routines are used for coulomb: FALSE > Table routines are used for vdw: FALSE > Cut-off's: NS: 0.45 Coulomb: 0.45 LJ: 0.45 > System total charge: 0.000 > > ------------------------------------------------------- > Program genbox, VERSION 4.0.5 > Source code file: ns.c, line: 2295 > > Fatal error: > One of the box vectors has become shorter than twice the > cut-off length or box_yy-|box_zy| or box_zz has become smaller than the > cut-off. > ------------------------------------------------------- > Thanks in advance/Jamie > > > On Thu, Aug 13, 2009 at 2:10 PM, Vitaly V. Chaban <[email protected]> > wrote: >> >> What is the box size and what is the cutoff displayed by genbox? >> >> On Thu, Aug 13, 2009 at 8:10 PM, Jamie Seyed<[email protected]> wrote: >> > Hi Vitaly, >> > Thanks for the answer. When I said far away means my pore was in one >> > corner >> > of vmd window and the water molecules in opposite corner (almost). >> > Anyways, >> > I tried to use your method but I think I am missing some parts... >> > I did: >> > (1)editconf -bt cubic -f conf.gro -o pore_edco.pdb -d 0.02 ---> seems >> > fine >> > (2)genbox -cp pore_edco.pdb -cs spc216.gro -o pore edco_b4em.pdb -p >> > topol.top here there is an error: one of the box vectors has become >> > shorter >> > than twice the cut-off length or box_yy-|box_zy| or box_zz has become >> > smaller than the cut-off. >> > >> > would you please let me know how I can fix the error (I don't see where >> > I >> > can change the cut-off !). Also am I doing right or I need a box of >> > water >> > first without introducing my molecule... >> > I appreciate to get more information and some help... Thanks a lot/Jamie >> > >> > >> > On Thu, Aug 13, 2009 at 12:21 PM, Vitaly V. Chaban <[email protected]> >> > wrote: >> >> >> >> Jamie, >> >> >> >> I didn't understand why you meant saying "waters far from the outside >> >> of the pore"... Far from outside, then where exactly? Maybe I just >> >> imagine your box incorrectly. >> >> >> >> To fill the pore with a solvent try to "deceive" genbox a little: >> >> 1) make a box (see editconf) in such a way that it contains only >> >> "inside" part of your pore. genbox will not report an error from its >> >> side. >> >> 2) add the solvent with genbox. >> >> 3) return to the original box size. >> >> 4) add the outside part. >> >> >> >> Vitaly >> >> >> >> > I want to know how can I use genbox to fill inside of the pore as >> >> > well >> >> > as a >> >> > layer outside. From the "man genbox" page I try to use -shell with a >> >> > negative value (?) but it put waters far from the outside of the pore >> >> > and I >> >> > think it does not care about the sign. It seems strange to me because >> >> > when I >> >> > had 10 10 10 in the last line of my f.gro, by a shell 0.5 or 0.2, I >> >> > got >> >> > a >> >> > layer of few molecule around the pore, but when I change it to 1. 1. >> >> > 1., >> >> > the >> >> > water molecules generated far away. I appreciate if someone tell me >> >> > (1) >> >> > how >> >> > I can add water inside the pore and (2) why changing the box size >> >> > will >> >> > give >> >> > a opposite result. Please advise..Thanks in advance/Jamie _______________________________________________ gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. 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