<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 style="FONT-SIZE: 12pt; FONT-FAMILY: times new roman, new york, times, serif">
<P style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif">dear Justin,</P>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif">tanks for your kindness.I would like to follow up what you say,but I want to have simulation without wraping.</DIV>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif">could these command be helpful?</DIV>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif">trjconv -s first1ns.tpr -f whatever_trajectory_you_want(xtc after 3ns simulation).xtc -pbc mol -center -o fit.gro</DIV>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif"> grompp -f md300.mdp -c fit.gro -p n.top -o md300.tpr -n n.ndx<BR> nohup mpirun -np 8 mdrun -s md300.tpr -o md300.trr -c md300.gro -g md300.log -e md300.edr&</DIV>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif">best regards<BR></DIV>
<DIV style="FONT-SIZE: 10pt; FONT-FAMILY: arial, helvetica, sans-serif"><BR>ana johari wrote:<BR>> dear user,<BR>> <BR>> Tanks for your advice,<BR>> <BR>> But the mdrun is know on the step of 33562880 but the protein was split at the first 1ns of MD. is <http://md.is/> it necessary to use “tpbconv” command and extract the *.tpr file just after first 1 ns and then use trjconv –ur compact as command.<BR>> <BR><BR>No. If the starting configuration had the protein properly centered in the box, then a simple:<BR><BR>trjconv -s first.tpr -f whatever_trajectory_you_want.xtc -pbc mol -center<BR><BR>should work to make molecules whole and center the protein in the box.<BR><BR>-Justin<BR><BR>> Best regards,<BR>> <BR>> <BR>> ------------------------------------------------------------------------<BR>> *From:* Justin A. Lemkul <<A href="mailto:jalemkul@vt.edu"
ymailto="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 2:52:53 PM<BR>> *Subject:* Re: [gmx-users] FW: protein split over boundary<BR>> <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> <mailto:<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> <mailto:<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>> <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>>>> 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>> <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>> <mailto:<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>> <mailto:<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>> <mailto:<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>> <mailto:<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>> <mailto:<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> <http://vt.edu/> | (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> <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 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>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]vt.edu | (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>-- 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>