Thanks for the advice <br>
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. <br>
problem cames only while running the minimization using the .tpr file <br>
<br>
For convenience, as mention earlier, following was the problem :<br>
...................<br>
Warning: 1-4 interaction between 1 and 9 at distance 8.443 which is larger than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation<br>
This usually means your system is exploding,<br>
if not, you should increase table-extension in your mdp file<br>
<br>
...................<br>
could you please suggest me some way out for this. <br>
<br>
Thanks<br>
<br>
With Regards <br>
Gurpreet<br>
<br>
<br><div><span class="gmail_quote">On 7/4/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Mark Abraham wrote:<br>>> Thanks Mark for your advice<br>>><br>>> I tried to run the simulation even by removing all the restraints as you<br>>> told but the same problem was coming.<br>>> In your second reply you asked me to check the topology file. I have a
<br>>> doubt in that, actually what are the things i should look at in the<br>>> topology<br>>> file. I have seen my topology file and the related .itp files also but i<br>>> did<br>>> not find anything unusual in that.
<br>>><br>>> Following are the contents of my Topology file:<br>>><br>>> ; Include forcefield parameters<br>>> #include "ffG43a1.itp"<br>>><br>>> ; Include chain topologies
<br>>> #include "aquapomut_grom_A.itp"<br>>> #include "aquapomut_grom_B.itp"<br>>><br>>> ; Include water topology<br>>> #include "spce.itp"<br>>><br>>> #ifdef POSRES_WATER
<br>>> ; Position restraint for each water oxygen<br>>> [ position_restraints ]<br>>>
; i funct
fcx fcy fcz<br>>> 1 1
1000
1000 1000<br>>> #endif<br>>><br>>> ; Include generic topology for ions<br>>> #include "ions.itp"<br>>><br>>> [ system ]<br>>> ; Name<br>>> Protein in water<br>
>><br>>> [ molecules ]<br>>> ; Compound #mols<br>>> Protein_A 1<br>>> Protein_B 1<br>>> SOL 71<br>>> CL- 6<br>>> SOL 14825
<br>><br>> Two regions of SOL doesn't sound like a good idea, but I won't swear it's<br>> the problem.<br><br>this is why I suggested grompp -maxwarn 0, because it will detect the<br>inconsistencies in names and tell you to fix it.
<br><br><br>><br>> Mark<br>><br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a><br><br><br>--<br>David van der Spoel, Ph.D.<br>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br><a href="mailto:spoel@xray.bmc.uu.se">
spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>_______________________________________________<br>gmx-users mailing list
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