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<div style="RIGHT: auto">Dear Tsjerk</div>
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<div style="RIGHT: auto">Thank you</div>
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<div style="RIGHT: auto">Sogol<VAR id=yui-ie-cursor></VAR></div>
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<DIV style="BORDER-BOTTOM: #ccc 1px solid; BORDER-LEFT: #ccc 1px solid; PADDING-BOTTOM: 0px; LINE-HEIGHT: 0; MARGIN: 5px 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; HEIGHT: 0px; FONT-SIZE: 0px; BORDER-TOP: #ccc 1px solid; BORDER-RIGHT: #ccc 1px solid; PADDING-TOP: 0px" class=hr contentEditable=false readonly="true"></DIV><B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Tsjerk Wassenaar <tsjerkw@gmail.com><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Kowsar Bagherzadeh <kw_bagherzadeh@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Wednesday, May 16, 2012 2:46 PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [gmx-users] Spherical shaped box<BR></FONT></DIV><BR>Hi Sogol,<BR><BR>You remove jumps over periodic boundary conditions, giving a<BR>continuous trajectory. That gives you a very nice view on diffusion in<BR>your system, which
happens to be equal in all directions. Hence, the<BR>end result looks spherical. But that's not the same as having a<BR>spherical box. If you draw the box in VMD or Pymol, you'll see it's<BR>still close to the original (triclinic) shape, but has become a bit<BR>small in relation to your molecules.<BR><BR>Cheers,<BR><BR>Tsjerk<BR><BR>On Wed, May 16, 2012 at 11:49 AM, Kowsar Bagherzadeh<BR><<A href="mailto:kw_bagherzadeh@yahoo.com" ymailto="mailto:kw_bagherzadeh@yahoo.com">kw_bagherzadeh@yahoo.com</A>> wrote:<BR>> Dear users,<BR>><BR>> I am doing Protein Ligand simulation, increasing temp. from 100, 200, to 300<BR>> K. after 1ns of simulation in 300 K, the protein jumps out of the box and<BR>> when I use the command<BR>><BR>> trjconv_mpi -f *.trr -s *.tpr -o *new.trr -pbc nojump<BR>><BR>> followed by<BR>><BR>> trjconv_mpi -f new*.trr -s *.tpr -o new*.pdb -dump 1000<BR>><BR>> the box
shape changes from dodecahedron to spherical. In Gromacs manual I<BR>> read ;<BR>><BR>> " There are several possible shapes for space-filling unit cells. Some, as<BR>> the rhombic dodecahedron and the truncated octahedron approach a spherical<BR>> shape better than a cubic box and are therefore more economical for studying<BR>> an (approximately spherical) macromolecule in solution, since less solvent<BR>> molecules are required to fill the box given a minimum distance between<BR>> macromolecular images....... ".<BR>><BR>> Does it mean that it is ok and I can continue the simulation or I have to<BR>> increase the box size? After simulation in 200 K the protein juped out of<BR>> the box but using the same command the problem was fixed, without changing<BR>> the box shape.<BR>> Thank you in advance for the help<BR>><BR>> Sogol<BR>><BR>><BR>> --<BR>>
gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>> http://lists.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at<BR>> <A href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=_blank>http://www.gromacs.org/Support/Mailing_Lists/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" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<BR><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar, Ph.D.<BR><BR>post-doctoral researcher<BR>Molecular Dynamics Group<BR>* Groningen Institute for Biomolecular Research and Biotechnology<BR>* Zernike Institute for Advanced Materials<BR>University of Groningen<BR>The
Netherlands<BR><BR><BR></DIV></DIV></div></body></html>