[gmx-users] mixing tabulated potential with force field for the AdResS

Jakub Krajniak jakub.krajniak at cs.kuleuven.be
Mon Feb 3 15:41:37 CET 2014


I am trying to run the system that is composite of the atomistic part 
and the coarse grained part. Together it should be coupled by the AdResS.
For the atomistic part I have already run the simulation with the opls 
force field. It run without issue and gave correct density under STP.
The coarse grained part is described by two tables, the bonded 
interaction by table_b1.xvg and the non-bonded interaction by 
table_A_A.xvg. This also run correctly. Under STP I am getting almost 
correct value of density.
Now, when it comes to coupling it together I am following the procedure 
from the 6.11 (user-manual). My index file contains the group for 
coarse-grained and group for all-atom molecules.
When I run the grompp -v -n I am getting warning:

"Using sigma/epsilon based combination rules with user supplied 
potential function may produce unwanted results"

I could skip it but I don't understand what is the meaning of this warning?

If I skip it then when I run the mdrun_d -v I am getting error with
information about missing table.xvg and tablep.xvg.
I don't understand why I have to provide the table for pair interaction? 
(it wasn't required in the all-atom case - assume that opls/ff handled it).
The same for the table.xvg file, the colombtype is set to cut-off.
I could probably provide empty table.xvg and tablep.xvg but still want 
to understand how it works.

Best regards,

Jakub Krajniak, Computer Science Department @ KU Leuven
mob. +32 477 688 404
room: 200a 01.41

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