hI<br><br>My -d parameter is 1.1 in editconf. Is that alright?<br><br>rakesh<br><br><div><span class="gmail_quote">On 3/13/07, <b class="gmail_sendername">Olivier Perin</b> <<a href="mailto:operin@pasteur.fr">operin@pasteur.fr
</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br><br>4ns becomes a long dynamic simulation. Sometimes during such a
<br>simulation, the system moves such a way that it "seems" to get out of<br>the water box.<br><br>In order to prevent this phenomen, you can use one parameter normally<br>used during a simulation in vaccum:<br>
<br>nstcomm = 500 ;<br><br>You can add this line to your mdp file before the grompp step. This is<br>the frequency for center of mass motion removal.<br><br>About the 2.2nm: if it is the real size of your box, I agree with the
<br>answer of Mark, the box is probably to short. But if it's your "-d"<br>parameter for editconf, it is largely sufficient.<br><br>Good Luck<br><br>Olivier<br><br>Mark Abraham a écrit :<br>> Rakesh Mishra wrote:
<br>>><br>>> When I run simulations on a 42 residue peptide with a box size of 2.2<br>>> nm , I find that after 4 ns , the peptide comes out of the box . Is<br>>> this a problem as far as the accuracy of the simulation results are
<br>>> concerned. Do the periodic conditions account for such cases? If not<br>>> , is there any suggestion as to how I may salvage my data without<br>>> having to start all over again .<br>><br>> The peptide can't "come out of the box" - the system is periodic. The
<br>> numbers in the trajectory file can be such that your visualization<br>> software will render an image that looks like the peptide comes out of<br>> the box, however. Look at the man page for trjconv and choose an
<br>> option appropriate for your situation and use that on the trajectory<br>> before visualizing.<br>><br>> By the way, a 42 residue peptide is almost certainly too large for<br>> such a box, even if it is a compact peptide. There are guaranteed to
<br>> be many water molecules (or even all of them) that are having<br>> non-bonded interactions with two images, which is unphysical.<br>><br>> Mark<br>> _______________________________________________<br>
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