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

[David van der Spoel]

gurpreet singh wrote:
> 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
> 

is 8.443 close to the size of your box? In that case it suggests that 
your molecules is split incorrectly.


> ...................
> 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 
> <mailto: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
>     <mailto:spoel at xray.bmc.uu.se>    spoel at gromacs.org
>     <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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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