[gmx-users] Regarding editconf

[Mark Abraham]

On 17/03/11, bipin singh  <bipinelmat at gmail.com> wrote:
> 
> 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?
> 
> 

It means no box is defined.


> 
> 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
> 
> 

At a minimum, you want no solvent atom to be able to see two images of your solute. So depending on your rcoulomb/rvdw/rlist regime, you are probably at the minimum that would be reasonable. If your globular protein expands at all, or can uncoil some loops, you might not have a sound model.


> 
> 
> 
> 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?
> 

The old box was bigger. Have a look at the relevant part of your input file.


> 2)Why the new length of box vectors decreased?And what does it mean?
> 

You implicitly told it a cubic box size you wanted with the -d flag, i.e. the size of protein plus the margin of 0.9nm. Whether that's a decrease is not relevant.


> 
> 3)How gromacs assign vectors length?If not provided in the editconf command.
> 

See above.


> 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.
> 

See genbox -h.

Mark
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