dear Justin, tanks for your kindness.I would like to follow up what you say,but I want to have simulation without wraping. could these command be helpful? trjconv -s first1ns.tpr -f whatever_trajectory_you_want(xtc after 3ns simulation).xtc -pbc mol -center -o fit.gro grompp -f md300.mdp -c fit.gro -p n.top -o md300.tpr -n n.ndx nohup mpirun -np 8 mdrun -s md300.tpr -o md300.trr -c md300.gro -g md300.log -e md300.edr& best regards
ana johari wrote: > dear user, > > Tanks for your advice, > > 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. > No. If the starting configuration had the protein properly centered in the box, then a simple: trjconv -s first.tpr -f whatever_trajectory_you_want.xtc -pbc mol -center should work to make molecules whole and center the protein in the box. -Justin > Best regards, > > > ------------------------------------------------------------------------ > *From:* Justin A. Lemkul <jalem...@vt.edu> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *Sent:* Fri, April 1, 2011 2:52:53 PM > *Subject:* Re: [gmx-users] FW: protein split over boundary > > > > ana johari wrote: > > Dear user, > > > > 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? > > > > 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. > > > 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? > > > > In principle, no, as long as your box does not significantly deform. Check >with g_mindist -pi. > > -Justin > > > tanks > > > > > > > > ------------------------------------------------------------------------ > > *From:* Tsjerk Wassenaar <tsje...@gmail.com <mailto:tsje...@gmail.com>> > > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> > > *Sent:* Fri, April 1, 2011 1:29:19 PM > > *Subject:* Re: [gmx-users] FW: protein split over boundary > > > > >http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > > -TAW > > > > On Fri, Apr 1, 2011 at 10:53 AM, anahita <ana_j0...@yahoo.com ><mailto:ana_j0...@yahoo.com> <mailto:ana_j0...@yahoo.com ><mailto:ana_j0...@yahoo.com>>> wrote: > > > > > > > > > > > > > > > From: anahita [mailto:ana_j0...@yahoo.com <mailto:ana_j0...@yahoo.com> ><mailto:ana_j0...@yahoo.com <mailto:ana_j0...@yahoo.com>>] > > > Sent: Friday, April 01, 2011 1:13 PM > > > To: 'gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org> ><mailto:gmx-users-requ...@gromacs.org <mailto:gmx-users-requ...@gromacs.org>>' > > > Subject: protein split over boundary > > > > > > > > > > > > Dear user, > > > > > > Hello, I appreciate if somebody help me. During the simulation of my >protein > > > I didn’t get any error but after 1ns of MD > > > > > > my molecule was split over boundary in cubic box. it means some part of >it > > > enter the other side of the box. > > > > > > At first,For decreasing the cost of simulation, in “editconf” command I >set > > > the number “d” on 0.9 to decease the box size. I want to mention that > > > during the calculation my rvdw is 1.4. > > > > > > I want to know instead of problem of visualization, the other things is > > > fine? > > > > > > Best regards. > > > > > > A. johari > > > > > > -- > > > gmx-users mailing list gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>>. > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > -- Tsjerk A. Wassenaar, Ph.D. > > > > post-doctoral researcher > > Molecular Dynamics Group > > * Groningen Institute for Biomolecular Research and Biotechnology > > * Zernike Institute for Advanced Materials > > University of Groningen > > The Netherlands > > -- > > gmx-users mailing list gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org>> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org> <mailto:gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org ><mailto:gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or >send it to gmx-users-requ...@gromacs.org ><mailto:gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
