Hi Omer,<br><br>My question was to how to avoid the "diffusion" of molecules out of the box during energy minimization and MD run? I think what you suggested here will just change the present trajectory into a new by using the pbc condition. <br>
<br>But i am wondering shouldnt this be done in MD calculation itself. It seems me to me that physics will be significantly different if i dont put the particles which go out of the box, back into the box. In that way the box will keep on expanding as i increase my simulation time and the calculated equilibirium properties wont be very meaningful and will fluctuate more than they really should. <br>
<br>By the way i am talking about long chain lipid molecules here and i am using an all bond constraint. <br><br>Amit<br><br><br><br><div class="gmail_quote">On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch <span dir="ltr"><<a href="mailto:omermar@gmail.com">omermar@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;"><div dir="ltr">Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help printed. Omer.<div class="im">
<br><div class="gmail_quote"><div> </div><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>I actually didnt realize this until i did a long simulation after which the trajectories of some of the atoms looked way out of the box dimensions. The co-ordinates of many atoms didnt lie in the box range. Although the output file contained the same box dimensions as I started with. Could someone help me in understanding what happened?</div>
<br></blockquote></div><br></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>