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

Mark Abraham Mark.Abraham at anu.edu.au
Thu May 7 03:57:42 CEST 2009

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?

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.


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