<p>Hi MKS,</p>
<p>The distance between the solute and the sides of the box is separate from the cutoffs. But, you want to have them large enough to avoid self-interaction across the PBC. So the distance has to be set larger than half the size of the cut-off. You probably shouldn't set it lower than 1nm though, as within that range the water molecules may still experience effects of the protei (ordering).</p>
<p>For the second part of your question, please refer to the manual and the wiki, as well as to the mailing list archives. </p>
<p>Cheers,</p>
<p>Tsjerk</p>
<p><blockquote type="cite">On Jan 13, 2011 7:59 AM, <<a href="mailto:kavya@rishi.serc.iisc.ernet.in">kavya@rishi.serc.iisc.ernet.in</a>> wrote:<br><br>Dear Gromacs users,<br>
<br>
I am new to gromacs. I want to simulate a system<br>
(protein) with a dodecahedron box in order to minimize<br>
the time.<br>
<br>
rlist = rcolumb = 1.2nm; (PME)<br>
rvdw = 1.1nm; rvdw_switch = 0 (using vdwtype = switch)<br>
<br>
so when giving the simulation box, should i give the<br>
value of -d as >=1.2nm?<br>
<br>
Does this same rule apply to a cubic box also?<br>
<br>
when I am using dodecahedron box with -d as 1.3nm, the waters<br>
added using the command:<br>
<br>
genbox -cp box-1-11.pdb -cs spc216 -p topol-1-11.top -o water-1-11.pdb<br>
<br>
Water box appears cubic and goes out of the dodecahedron box used.<br>
Why is this happening and what is the solution for this? Kindly<br>
give some suggestions.<br>
<br>
Thanks in advance<br>
MKS<br>
<br>
<br>
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