[gmx-users] Re: solvation

[Vitaly V. Chaban]

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<jamie.seyed at gmail.com> 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 <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