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<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>Dear user,</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>Tanks for your attention ,I read about trjconv,but I want to know is it necessary <SPAN style="mso-spacerun: yes"> </SPAN>to back to the exact fram befor molecule split happens and then center the molecule by trjconv command?</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>The other point,if you attention to my value”edit conf <SPAN style="mso-spacerun: yes"> </SPAN>d=0.9 and during MD rvdw=1..4” is it broke the rule of periodic boundary condition or not?</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>tanks</FONT></P><BR></DIV>
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<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Tsjerk Wassenaar <tsjerkw@gmail.com><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Discussion list for GROMACS users <gmx-users@gromacs.org><BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Fri, April 1, 2011 1:29:19 PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [gmx-users] FW: protein split over boundary<BR></FONT><BR>http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions<BR><BR>-TAW<BR><BR>On Fri, Apr 1, 2011 at 10:53 AM, anahita <<A href="mailto:ana_j0000@yahoo.com" ymailto="mailto:ana_j0000@yahoo.com">ana_j0000@yahoo.com</A>> wrote:<BR>><BR>><BR>><BR>><BR>> From: anahita [mailto:<A href="mailto:ana_j0000@yahoo.com" ymailto="mailto:ana_j0000@yahoo.com">ana_j0000@yahoo.com</A>]<BR>> Sent: Friday, April 01, 2011 1:13 PM<BR>> To: '<A href="mailto:gmx-users-request@gromacs.org"
ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>'<BR>> Subject: protein split over boundary<BR>><BR>><BR>><BR>> Dear user,<BR>><BR>> Hello, I appreciate if somebody help me. During the simulation of my protein<BR>> I didn’t get any error but after 1ns of MD<BR>><BR>> my molecule was split over boundary in cubic box. it means some part of it<BR>> enter the other side of the box.<BR>><BR>> At first,For decreasing the cost of simulation, in “editconf” command I set<BR>> the number “d” on 0.9 to decease the box size. I want to mention that<BR>> during the calculation my rvdw is 1.4.<BR>><BR>> I want to know instead of problem of visualization, the other things is<BR>> fine?<BR>><BR>> Best regards.<BR>><BR>> A. johari<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>> http://www.gromacs.org/Support/Mailing_Lists/Search 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>-- <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>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org"
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