<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
For quite a long time I had the feeling that trjconv doesn't resolve
all situations. Following the very recent discussion between Roland
Schutz and Tsjerk, I'm not sure there is an immediate solution. Ad hoc
approaches such as preparation of tpr files from intermediate snapshots
were useful for me in some cases, so you can try these. For
calculations of distances you can sometimes calculate the shift and
apply an a posteriori fix, but that won't work for visualisation and
isn't a robust solution. I don't think it has anything to do with the
MARTINI FF.<br>
<br>
Ran.<br>
<br>
maria goranovic wrote:
<blockquote
cite="mid9024f1330911060137t620432efh73b4ffde5737e413@mail.gmail.com"
type="cite">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 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><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><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><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> <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>
-Maria<br>
-- Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a
href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/"
target="_blank">http://www.gromacs.org/mailing_lists/</a>users.php<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br>
Please don't post (un)subscribe requests to the list. Use thewww<br>
interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
------------------------------------------------------------------------<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540)
231-9080<br>
<a
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to <a href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
</div>
</div>
Please don't post (un)subscribe requests to the list. Use thewww
interface or send it to <a href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.
<div>
<div> <br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</div>
</div>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the <br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></blockquote>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the <br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></blockquote>
</div>
</div>
</div>
<br>
</div>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org"
target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the <br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a></blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search"
target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a
href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>
<a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a>
Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.
Can't post? Read <a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></pre>
</blockquote>
<br>
</body>
</html>