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 <[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 > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
