[gmx-users] -table option in mdrun

Yang Ye leafyoung81-group at yahoo.com
Wed Mar 9 04:34:07 CET 2005



I am a bit coarse-grain MD with one "atom" of Van der Waals radius 50A of
charge -200 in the center and counter-ions of charge +1 (radii 1A) spreading
around. After trying with specifying LJ parameters according to 


r = power(2,1/6)*sigma

epsilon = 0.001 //I would like to have my "atoms" drop sharply at 100A, 52A,
or 2A


I found that they did not play a role in simulation (the model collapsed or
exploded). Then I came across of the option of -table in mdrun in supplying
custom VDW/Coulomb potential table (together use with coulombtype=User in


The example files under /usr/local/gromacs/share/top/table6-12.xvg shows
that there is seven columns.


My question is that since I have several types of interaction:





How can I supply potential tables to them repectively? Thanks.



Yang Ye

Computational Biology Lab

School of Biological Sciences

Nanyang Technological University


Tel: 65 6316 2884


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