[gmx-users] Re: solvation

Jamie Seyed jamie.seyed at gmail.com
Thu Aug 13 20:23:14 CEST 2009 

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 <vvchaban at gmail.com>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<jamie.seyed at gmail.com> 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 <vvchaban at gmail.com>
> > 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
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