[gmx-users] rvdw parameters

[Anton Feenstra]

"Shrivastava, Indira (NCI)" wrote:
> 
>  Hi All,
> 
>  I have two simulations of a protein in different slabs:
>  one is in an octane slab and other is in a POPE bilayer.
>  The electrostatic calculations in both the simulations were done by
>  the CUTOFF method, with rcoulomb of 1.8.
>  But for the octane slab,I used rvdw of 1.0 and for the POPE bilayer, rvdw
> was 1.4
> Can I compare the protein structural characteristcs of these
>  two simulations? Or would it not be right?

Of course you can compare it. ;-)

But you will never know whether differences arise from the system 
or from the cut-off values. That said, the changes do not appear to
be too drastical, so I would not expect noticable differences in 
the response of your system as a result of the cut-off differences.

See other comments below...

> Also, does anyone know what are the 'ideal' parameters for rcoulomb and rvdw
> for simulations where electrostatics is computed using the PME method?

No ideal, just only one correct option: the parameters must be exactly
what they were during forcefield development. This is 0.8/1.4 (twin-range)
for the G42* forcefields, both for coulomb and rvwd. Thechnically, using
PME in stead of twin-range is not correct either, but it won't hurt and
for some (heavily charged) systems it is inevitable to use PME.
Especially the short-range cutoff (0.8) *SHOULD* *NEVER* *BE* *CHANGED*.
For the long range it is not so critical, but you would rather use 0.8/PME
in stead of increasing the 1.4 long range cut-off.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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