[gmx-users] box of methanol

[K.A. Feenstra]

Luca Monticelli wrote:
> 
> I used the G43a1 force field, with
> cut-offs 0.8/1.4 (Gromos-96 was
> parameterized with these twin-range
> cut-offs, right?) and NPT conditions;
> box size is approximately 4.3*4.3*4.3,
> timestep=2fs, nstlist=5, no constraints,
> compressibility= 4.575e-4; total time is 5 ns.

Right: 0.8/1.4. Rest sounds good, too.

> These are the results.
> It takes ~500 ps for the pressure to become relatively stable.
> Excluding the initial 500 ps, the average d=749, with
> an RMSD of 3.9.

Sounds good, too...

> If I change the cut-offs to 0.9/1.4,  leaving all other
> parameters identical, I find d=782, with
> an RMSD of 3.5. Not bad, the error is only ~1.1%.

Yes, except that I'd advise strongly against using the
cut-off parameter to adjust your density to the exp'tal
value. Rather, you should probably adjust the lennard-
jones parameters for methanol-methanol interactions.

Your results in general will be extremely sensitive especially 
to the short-range cut-off. The change from 0.8 to 0.9 seems
small, and maybe negligible, but it will probably add up to
a fairly large cumulative effect. Remember that these effects
are counteracted by details in the parameterization, but if
you change the effects (by changing the cut-off), that no 
longer holds. Also keep in mind that a change in radius of
about 10-15% will give a 40-45% change in the sphere surface,
and hence a potentially equally large change in sum of
interactions...

> Now I am running a couple of tests to check
> for dependency on the box size; I
> already run 1 ns on a smaller box (about
> 3*3*3), and the results seem to be very
> similar, so far.

Also sounds good.

> If anybody is interested in using this
> box, just let me know.

It might be a good idea to upload it to the Gromacs site.


-- 
Groetjes,

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