[gmx-users] modify lennard jones parameters to time-dependent

David van der Spoel spoel at xray.bmc.uu.se
Thu May 7 07:18:08 CEST 2009

Mark Abraham wrote:
> Xinghua Shi wrote:
>> Dear all,
>> Is there any way to modify the LJ potential as a time dependent value,
>> e.g. V(r)=4*e(t)*((sigma/r)^12-(sigma/r)^6), here e(t) is
>> time-dependent, for instance, e(t)=e0*cos(w*t)? If the code needs to
>> be modified, which C file should I find?

In your example you would also change the sign of the potential, which 
might give interesting effects.

However you can also use external forces using the accelaration options 
in the mdp file, which might not be what you want though.

> Simplest would be to generate a series of suitable LJ tables and pass 
> the correct table to the non-bonded kernel to use for the table lookups, 
> however that will be slower than computed LJ. Otherwise, you have to 
> modify the non-bonded kernels. There's a spare parameter you can use to 
> pass in the current value of e(t). Search the mailing list for advice on 
> modifying non-bonded kernels - I've given some before.
> Mark
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David van der Spoel, PhD, Professor of Biology
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://folding.bmc.uu.se

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