[gmx-users] -table option in mdrun

[David van der Spoel]

On Wed, 2005-03-09 at 11:34 +0800, Yang Ye wrote:
> 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.
You can only have one potential form for all interactions, which you can
modulate with parameters. 50 Å particles will be difficult to combine
with 1 Å. You could also consider modeling your 50 Å particle by
something like a bucky ball, with smaller atoms.

> 
>  
> 
> Regards,
> 
> Yang Ye
> 
> Computational Biology Lab
> 
> School of Biological Sciences
> 
> Nanyang Technological University
> 
> Singapore
> 
> Tel: 65 6316 2884
> 
>  
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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