[gmx-users] Tabulated soft-core potential, Ewald and free energy

[Anton Feenstra]

Filip Ryjácek wrote:
> 
> 
> Hi all,
> I am using soft-core approach for free energy calculation in GORMACS 
> (works wery well, comparing to AMBER/gibbs for example!), and I have 
> encountered two problems:
> 
> a) As show in output and in do_fnbf() and do_14(), GROMACS has only 
> tabulated routines for free-energy coulomb and LJ interactions (inl3301 
> and inl3302). In manual v3.1.1 on page number 122 is written: "Note that 
> table lookup is significantly slower than computation of the most simple 
> LJ and C interaction". So I guess GROMACS is slower for free energy 
> calc. than for mol. dynamics! Is there any technical/theoretical reason 
> for that?
> 
> b) I don't understand exactly the 'FEP_TABLE_LENGTH' variable. Why is it 
> set to 5nm? Is it something like cutoff?

This is Davids & Eriks hometurf, but since they have apparently not yet
answered, I'll give it a shot.

The 'most simple LJ and C' interaction, are implemented in assembly
(on Pentiums) or come from optimized C or Fortran libraries (on SGI,
IBM etc.). Since implementing the free energy code in assembly is not
feasible (too much work is an understatement). Reason is this soft-
core potential, which is much more complicated than 1/r^6 or so.
So then, the table lookup is faster than the calculating this soft-core
on the inner loops. No way around, as long as you want soft-core.

Don't know about point 'b)'.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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