So lets say that I delete the first frame from the trajectory in which some atoms might have been outside the box. Everything should be within the box once the simulation starts (from the second frame onwards)? So the procedure should work if the reference structure is the second frame? I have tried that, and it fails as well. <br>
<br><div class="gmail_quote">On Thu, Nov 5, 2009 at 4:40 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div style=""><div><br></div><div>The nojump option will not apply the pbc when an atom is crossing the </div><div>box boundaries ... in your case your bilayer should definitely be in the </div><div>center of your box and all the atoms in !!!! If not ot course it does not work!</div>
<div><div></div><div class="h5"><div><br></div><div><div><div>On Nov 5, 2009, at 4:33 PM, maria goranovic wrote:</div><br><blockquote type="cite">my starting structure looks quite all right to me. everything is in the box (except the tails of some lipids) .. wonder whats wrong. thank you verymuch for helping<br>
<br><div class="gmail_quote">On Thu, Nov 5, 2009 at 4:04 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>></span> wrote:<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br><div><div><div>On Nov 5, 2009, at 4:00 PM, maria goranovic wrote:</div> <br><blockquote type="cite">Hi Xavier,<br><br>Thanks for the clear instructions. The bilayer is not in one piece in the z direction after the -pbc nojump for some reason. <br>
</blockquote></div>the problem might be from your starting structure, everything should be in the box! </div> <div>Or you may be facing strange/funny/incomprehensible behavior ... <div><div></div><div><br><blockquote type="cite">
<br>after the third step, the water is in the right place, but the bilayer has expanded to periodic boxes in the xy plane. so the center of mass of the lipid molecules is not really being centered in the box ? <br> <br><br>
<div class="gmail_quote">On Thu, Nov 5, 2009 at 3:34 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div><br></div>you need to do:<div><br></div><div>1- trjconv -pbc nojump; this keeps your bilayer in one piece on the z direction<br><div><div>2- trjconv -center; using the bilayer to center and the system as output; this will </div>
<div>translate your bilayer on the z axis and normally not modify it on the xy plan. </div><div>3- trjconv -pbc mol; will put your lipids in one piece in the box; I believe this </div><div>step cn be coupled to the previous quite safely.</div>
<div><div></div><div><div><br></div><div>On Nov 5, 2009, at 3:23 PM, maria goranovic wrote:</div><br><blockquote type="cite">One more note about -pbc nojump. I typically use -pbc mol. Using pbc nojump succeeds in keeping the center of the bilayer at 0 0 0, but the atoms have moved way out of the simulation box resulting in a dilute system<br>
<br> <div class="gmail_quote">On Thu, Nov 5, 2009 at 2:31 PM, maria goranovic <span dir="ltr"><<a href="mailto:mariagoranovic@gmail.com" target="_blank">mariagoranovic@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Centering on one atom has a problem that the lipid diffuses in the plane of the membrane, and as a result, the entire system starts to center around the lipid resulting in a simulation box which translates a lot in the bilayer plane. <br>
<br>The splitting is not a problem, yes. But during the simulation period when the bilayer is not split, it diffuses quite a bit along the bilayer normal (after use of -pbc mol, and centering around the lipid center of mass). a plot of the lipid center of mass shows the bilayer diffusing along z, when its not split.<div>
<div></div><div><br> <br><div class="gmail_quote">On Thu, Nov 5, 2009 at 2:25 PM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><br> On Nov 5, 2009, at 2:02 PM, Justin A. Lemkul wrote:<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> <br> maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> I did use -pbc nojump, but that does not help<br> </blockquote> <br> What about entering on a central lipid tail atom, I suggested some time ago? The bilayer probably just splits across periodic boundaries, so this is not really a problem; just a visualization artefact.<br>
</blockquote></div> The splitting is not a problem and I think that centering using one lipid (tail) won't change the problem if<br> the bilayer is cut half! Or the -pbc mol should be applied ...<div><div></div><div>
<br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <br> -Justin<br> <br> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The drift is about 1 nm per 10 microseconds .<br> (this is a martini simulation)<br> On Thu, Nov 5, 2009 at 1:02 PM, XAvier Periole <<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a> <mailto:<a href="mailto:x.periole@rug.nl" target="_blank">x.periole@rug.nl</a>>> wrote:<br>
On Nov 5, 2009, at 12:09 PM, maria goranovic wrote:<br> Hello All (and especially Berk)<br> This is an update of the problem that I was facing earlier. I<br> used to tau_p of 3.0 ps, and the problem does not go away, the<br>
bilayers still drifts in the simulation box. So this is<br> probably a bug then?<br> How much is the drift (nm/ns)? Did you use removal of center of mass<br> of the entire system of<br> bilayer/solvent separately?<br>
I still cannot understand how to put the bilayer back into the<br> center of the simulation box. As suggested by Justin, I tried to<br> use just one tail atom of a lipid for centering, but that did<br> not work either.<br>
I noticed that my bilayer, which is initially at the center of<br> the simulation box, separates into two leaflets at the box edges<br> from the very first step of the simulation itself, but i am not<br>
able to correct that using the -center and -boxcenter zero<br> options. Can someone please make a suggestion and help?<br> You have to do use -pbc nojump first and then center ...<br> Thank you so much<br>
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