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

[Peyman Yamin]

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