[gmx-users] Regarding editconf

[bipin singh]

I have some questions regarding editconf:

1)If we did'nt mentioned -box parameters,the *default vectors are 0 0
0*, why it is zero and what does it mean?
2)How to determine distance between the solute and the box, is it
appropriate to take it 0.9 nm for
a globular protein of 179 amino acids.
After running editconf using the command
*editconf -bt cubic -f 1.pdb -o 2.pdb -c -d 0.9*

I got the following output:

Read 3256 atoms
Volume: 515.892 nm^3, corresponds to roughly 232100 electrons
No velocities found
    system size :  4.217  4.721  4.631 (nm)
    diameter      :  5.270               (nm)
    center          :  1.974  2.562  0.035 (nm)
    box vectors  :  7.602  7.602 10.309 (nm)
    box angles   :  90.00  90.00 120.00 (degrees)
    box volume  : 515.89               (nm^3)
    shift            :  1.562  0.973  3.500 (nm)
new center       :  3.535  3.535  3.535 (nm)
new box vectors :  7.070  7.070  7.070 (nm)
new box angles  :  90.00  90.00  90.00 (degrees)
new box volume  : 353.45               (nm^3)

I have some question regarding this output:
1)Why new box volume decreased?And what does it mean?
2)Why the new length of box vectors decreased?And what does it mean?
3)How gromacs assign vectors length?If not provided in the editconf command.
4)How gromacs place solvent inside the box(genbox) , I mean using which
method and how gromacs determine the the number of solvent to be placed
inside the box.

-----------------------
*Regards,*
Bipin Singh
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110317/d1e88714/attachment.html>