On 17/03/11, bipin singh <[email protected]> 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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