[gmx-users] -table option in mdrun

[Yang Ye]

Hi,

 

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
md.mdp).

 

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:

50A-50A

50A-1A

1A-1A

 

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

 

Regards,

Yang Ye

Computational Biology Lab

School of Biological Sciences

Nanyang Technological University

Singapore

Tel: 65 6316 2884

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050309/653ad84d/attachment.html>