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 Thanks and regards Pooja -- Quaerendo Invenietis-Seek and you shall discover.
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