<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>
<DIV>dear user,</DIV>
<DIV>
<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>Tanks for your advice,</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>But the mdrun is know on the step of 33562880 but the protein was split at the first 1ns of <A href="http://md.is/" target=_blank><SPAN class=yshortcuts id=lw_1301656865_0><FONT color=#0000ff>MD. is</FONT></SPAN></A> it necessary to use “tpbconv” command and extract the *.tpr file just after<SPAN> first </SPAN>1 ns and<SPAN> </SPAN>then use trjconv –ur compact as command.</FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 10pt"><FONT face=Calibri>Best regards,</FONT><BR></P></DIV></DIV>
<DIV style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif"><BR>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif"><FONT face=Tahoma size=2>
<HR SIZE=1>
<B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Justin A. Lemkul <jalemkul@vt.edu><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 2:52:53 PM<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [gmx-users] FW: protein split over boundary<BR></FONT><BR><BR><BR>ana johari wrote:<BR>> Dear user,<BR>> <BR>> Tanks for your attention ,I read about trjconv,but I want to know is it necessary to back to the exact fram befor molecule split happens and then center the molecule by trjconv command?<BR>> <BR><BR>If the protein starts in the center of the box, just use trjconv in conjunction with your original .tpr file. A suggested trjconv workflow is on the page Tsjerk pointed you to.<BR><BR>> The other point,if you attention to my value”edit conf d=0.9 and during MD
rvdw=1..4” is it broke the rule of periodic boundary condition or not?<BR>> <BR><BR>In principle, no, as long as your box does not significantly deform. Check with g_mindist -pi.<BR><BR>-Justin<BR><BR>> tanks<BR>> <BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> *From:* Tsjerk Wassenaar <<A href="mailto:tsjerkw@gmail.com" ymailto="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</A>><BR>> *To:* Discussion list for GROMACS users <<A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>><BR>> *Sent:* Fri, April 1, 2011 1:29:19 PM<BR>> *Subject:* Re: [gmx-users] FW: protein split over boundary<BR>> <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> <mailto:<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> <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> <mailto:<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> <mailto:<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> <mailto:<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>> gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A> <mailto:<A href="mailto:gmx-users@gromacs.org" ymailto="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/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> <mailto:<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 <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR>> <BR><BR>-- ========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<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>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<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><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/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 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 <A href="http://www.gromacs.org/Support/Mailing_Lists" target=_blank>http://www.gromacs.org/Support/Mailing_Lists</A><BR></DIV></DIV></div></body></html>