[gmx-users] mdrun crashed with tables

[Sai Pooja]

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 <Mark.Abraham at anu.edu.au>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
>
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