[gmx-users] Setup Box Size

[Anton Feenstra]

Nuno R. L. Ferreira wrote:

> From: "Anton Feenstra" <feenstra at chem.vu.nl>
> 
>>I usually take the distance between protein and box-edge slightly larger
> 
> than
> 
>>the largest of rvdw or rcoul (which are always equal for me anyway), so
> 
> for the
> 
>>usual rvdw=rcoul=1.4 for the Gromos 43a1 ff, I use 'editconf -d 0.8 -bt
> 
> dode'.
> 
> 
> So, the answer to my previous question posed to J. Kerrigan is: protein
> /protein distance, hence -d > 0.5*("largest of rvdw or rcoul ").
> Right?

No, the distances is from protein to box-edge, which makes the protein-
protein distance twice that. A simple '1d pbc' example may clarify:

	|	PPP	|	QQQ	|

'PPP' is the 'real' protein, 'QQQ' one of its images. '|' is the box edge.
Setting '-d' to 0.8, will keep the box 0.8 nm away from the protein, and
so the 'PPP'-'QQQ' distance will be about 1.6nm, larger than the cutoff.

> BTW, why so many people talk about the advantages of using PME, but still
> use coulombtype = cuttof?
> Time computational cost? Bad scalling in parallel runs?
> I assume that rvdw=rcoul=1.4 means that you're doing cutoff for vdw and
> coulomb.

Yes it does. The reason is simple: I've always used it up to now, and
it works for me. I'm considering switching to PME, but for the running
work I like to stay consistent with previous simulations. Actually, I
just started some pilot runs on a (heavily charged) peptide with PME.
Now I'll have to learn how to add counter-ions... ;-)


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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