[gmx-users] creating a box from a single molecule

[Tsjerk Wassenaar]

Hi Peyman,

What about using genconf?
Start off with one octanol in a box (-d 0.0) and use 'genconf -nbox 6
6 6' to obtain a box containing 216 of them. You can even add random
rotations. Then equilibrate.

Hope it helps,

Tsjerk


On Tue, May 27, 2008 at 7:03 PM, Peyman Yamin
<Peyman.Yamin at cbi.uni-erlangen.de> wrote:
> Dear gmx users,
>
> Note: this is probably extremely a beginner's problem! But I did my best to
> solve it, in vain!
>
> I have an irritating problem concerning creation of a box of solvent, say
> octanol, when I have a .pdb/.gro file for a single octanol molecule.
> I try genbox with -ci and -nmol after I make a box around a single molecule
> with editconf.
>
> First I try as stated in the genbox's help to make a box of solvent with -cs
> and -box:
>
> 1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and -cp
> with a structure file with a box, but without atoms.
>
> I make a box of octanol, with one molecule, and then try to use the same
> molecule as -cs. genbox adds nothing to the box firther.
>
>
> editconf -f octanol.pdb -o EM/b4EM.gro -box 4 4 4 -c
> genbox -ci b4EM.gro -nmol 243 -vdwd 0.2 -o box.gro -box 4 4 4
>
> First I don't know what is -vdwd exactly and how it differs from -rvdw of
> genbox?  is it the cutoff? is it the vdw radius of some atoms? is it the
> minimum distance atoms would be allowed to have from eachother? I calculate
> 243 molecules myself, to approximately correspond to the density of octanol.
>
> When I look a box.gro, I see that - with vmd - there are unwanted bonds
> between atoms! that is some are very near to eachother! when I then try a
> very simple Energy Minimization step, witht he hope they will keep distance,
> I understand that they are really in trouble:
>
> Step=  110, Dmax= 1.1e-01 nm, Epot=  9.86243e+05 Fmax= 7.43582e+05, atom= 1272
> Warning: 1-4 interaction between 1272 and 1275 at distance 1.056 which is
> larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> Step=  111, Dmax= 1.3e-01 nm, Epot=  9.66300e+05 Fmax= 2.69946e+04, atom= 1815
>
> I have no problem with boxes of water, as created with the help of spc, and
> indeed, I did many simulations with it! But I should I also make boxes of
> other molecules and it's a long time I'm stuck in it! It would be a great
> help if one could help me out of it, to know how to insert atoms in a box in
> safe way so that they won't overlap. Or basically, how did one once create
> spc215.gro!?
>
> Thanks in advance,
> Best regards
> Peyman
>
> --
> Peyman Yamin
> Lehrstuhl fuer Thermische Verfahrenstechnik
> Universitaet Erlangen-Nuernberg
> Egerlandstr. 3
> 91058 Erlangen
> Phone: +49(0) - 9131 - 85 27671
> Mailto: peyman.yamin at cbi.uni-erlangen.de
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623