[gmx-users] Setup Box Size

Anton Feenstra feenstra at chem.vu.nl
Tue Feb 10 08:45:06 CET 2004

Nuno R. L. Ferreira wrote:
> BTW, what do you (all gmx users) think we should do if at certain point of
> the simulation the box becomes "too short" to have a protein not seeing its
> periodic images? Stop the run, search a frame to begin a new md where
> there's not yet pbc problems, perhaps center the protein in the box, and
> continue from here?  Is it possible to increase the box size at certain
> frame (adding more solvent), without having big energetic problems at the
> interface between the old box edge and the new solvent layer, nor affecting
> the protein stability?

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'.

There is an option to g_mindist, '-pi' IIRC, that will calculate the shortest
periodic distance of a group of atoms with 'itself'. That way it is easy to
check if, and where, in a run your protein 'sees itself'. Be aware that, since
distances to 26 images must be calculated, this option tends to be very slow
(and it was never optimized for performance). But, you can use a large '-dt'.

As for increasing box-size, it is possible to 'multiply' your solute + solvent
system simply using genconf, but you may add up with parts of your solute
multiplied as well, so you'll have to remove that again manually. It would be
nice to have an option to stack 'spc216' water cubes onto your existing
solvent + solute system, preferably after re-centering the solute to be in
the middle of the solvent box to minimize the effect of the new solvent-


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | 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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