Hi all, 1) added -table tablefile1 -table tablefile2 etc.. to mdrun command ... 2)Increased table-extension parameter from 0.0 to 1.0 and added those values to the table too... Works now!
Thanks Mark and ms! Pooja On Tue, Nov 23, 2010 at 7:03 PM, Mark Abraham <[email protected]>wrote: > On 24/11/2010 8:42 AM, Sai Pooja wrote: > >> Hi, >> I run a simulation of a protein in water(tip3p) system using charmm >> forcefield. I have specified the following energy groups: >> Protein SOL and energy group tables Protein SOL SOL SOL. I set Coulombtype >> to User and VdW to Cut-off. I then generate tables as specified in the >> manual. To test the validity of these tables, I standard Coulomb and LJ6,12 >> tables. >> I generate 4 tables - table.xvg, table_Protein_SOL.xvg, table_SOL_SOL.xvg >> and tablep.xvg (all identical) >> When I run grompp I get no errors. When I run mdrun, it stops after the >> first step as LINCS fails to converge. >> I run the same simulation by changing the Coulombtype to Cut-off and >> without the tables and it runs. >> Can you suggest what could be going wrong? >> (python script) >> Command used: cmd += '(%s/mdrun_mpi -s rex_%d.tpr -e rex_%d -c >> after_rex_%d -cpi restart%d -cpo restart%d -cpt 0.1 -append -g rexlog%d -x >> rextraj%d -table table.xvg table_Protein_SOL.xvg table_SOL_SOL.xvg -tablep >> tablep.xvg >/dev/null); ' %(GROMPATH,i,i,i,i,i,i,i) >> I tried this in two ways - >> 1) specified [ nonbonded_param ] for all Protein atoms and tip3p atoms >> 2) Not specifying them separately >> > > What does the .log file report about the tables it's read? I don't know how > the -table mechanism works, but its conceivable that you need -table file1 > -table file2 -table file3. > > Mark > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Quaerendo Invenietis-Seek and you shall discover.
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