<font face="Arial"><font size="3"><pre>I have some questions regarding editconf:<br><br>1)If we did'nt mentioned -box parameters,the <b>default vectors are 0 0 0</b>, why it is zero and what does it mean?<br>2)How to determine distance between the solute and the box, is it appropriate to take it 0.9 nm for<br>
a globular protein of 179 amino acids.<br>After running editconf using the command<br><b>editconf -bt cubic -f 1.pdb -o 2.pdb -c -d 0.9</b><br></pre></font></font><span style="color: rgb(51, 51, 255);"><span style="color: rgb(0, 0, 0);">I got the following output:<br>
<br style="color: rgb(0, 0, 0);"></span><span style="color: rgb(0, 0, 0);">Read 3256 atoms</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">Volume: 515.892 nm^3, corresponds to roughly 232100 electrons</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);">No velocities found</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"> system size : 4.217 4.721 4.631 (nm)</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"> diameter : 5.270 (nm)</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);"> center : 1.974 2.562 0.035 (nm)</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"> box vectors : 7.602 7.602 10.309 (nm)</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);"> box angles : 90.00 90.00 120.00 (degrees)</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"> box volume : 515.89 (nm^3)</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);"> shift : 1.562 0.973 3.500 (nm)</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">new center : 3.535 3.535 3.535 (nm)</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);">new box vectors : 7.070 7.070 7.070 (nm)</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">new box angles : 90.00 90.00 90.00 (degrees)</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);">new box volume : 353.45 (nm^3)</span><br style="color: rgb(0, 0, 0);"><br><span style="color: rgb(0, 0, 0);">I have some question regarding this output:</span><br style="color: rgb(0, 0, 0);">
<span style="color: rgb(0, 0, 0);">1)Why new box volume decreased?And what does it mean?</span><br style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">2)Why the new length of box vectors decreased?And what does it mean?<br>
3)How gromacs assign vectors length?If not provided in the editconf command.<br>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.<br style="color: rgb(0, 0, 0);">
</span><br>-----------------------</span><br style="color: rgb(51, 51, 255);"><i><span style="color: rgb(51, 51, 255);">Regards,</span></i><br style="color: rgb(51, 51, 255);"><span style="color: rgb(51, 51, 255); font-family: garamond,serif;">Bipin Singh</span><br>
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