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* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> 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.
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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