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
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