[gmx-users] [Fwd: How simulate two peptides in a box?]

[gurpreet singh]

Thanks for the advice
In my case no problem is coming while running the grompp, no warning is
coming. i could able to generate .tpr file without any error.
problem cames only while running the minimization using the .tpr file

For convenience, as mention earlier, following was the problem :
...................
Warning: 1-4 interaction between 1 and 9 at distance 8.443 which is larger
than the 1-4 table size 1.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file

...................
could you please suggest me some way out for this.

Thanks

With Regards
Gurpreet


On 7/4/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Mark Abraham wrote:
> >> Thanks Mark for your advice
> >>
> >>  I tried to run the simulation even by removing all the restraints as
> you
> >> told but the same problem was coming.
> >> In your  second reply you asked me to check the topology file. I have a
> >> doubt in that, actually what are the things i should look at in the
> >> topology
> >> file. I have seen my topology file and the related .itp files also but
> i
> >> did
> >> not find anything unusual in that.
> >>
> >> Following are the contents of my Topology file:
> >>
> >> ; Include forcefield parameters
> >> #include "ffG43a1.itp"
> >>
> >> ; Include chain topologies
> >> #include "aquapomut_grom_A.itp"
> >> #include "aquapomut_grom_B.itp"
> >>
> >> ; Include water topology
> >> #include "spce.itp"
> >>
> >> #ifdef POSRES_WATER
> >> ; Position restraint for each water oxygen
> >> [ position_restraints ]
> >> ;  i funct       fcx        fcy        fcz
> >>    1    1       1000       1000       1000
> >> #endif
> >>
> >> ; Include generic topology for ions
> >> #include "ions.itp"
> >>
> >> [ system ]
> >> ; Name
> >> Protein in water
> >>
> >> [ molecules ]
> >> ; Compound        #mols
> >> Protein_A           1
> >> Protein_B           1
> >> SOL                71
> >> CL-                 6
> >> SOL             14825
> >
> > Two regions of SOL doesn't sound like a good idea, but I won't swear
> it's
> > the problem.
>
> this is why I suggested grompp -maxwarn 0, because it will detect the
> inconsistencies in names and tell you to fix it.
>
>
> >
> > Mark
> >
> >
> > _______________________________________________
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>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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