On Wed, Feb 16, 2011 at 1:00 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 16/02/2011 10:30 PM, ifat shub wrote: > > Hi Tsjerk, > Thank you for your reply. > I am aware of the trajconv option but I wanted to know if there is a way to > avoid these kind of jumps over the periodic boundaries during the mdrun and > not post process? > > No. mdrun does not know in advance what your visualization requirements are, > and frankly there are better things to do with expensive compute cluster > time. Post-processing a small number of frames elsewhere is much better use > of resources. >
Or: No. mdrun takes the internal representation that is most efficient, and there are better things to do with expensive compute cluster time than writing out a trajectory without jumps, which might not even be what you want in the end. :) Tsjerk > Mark > > >> message: 4 >> Date: Wed, 16 Feb 2011 11:19:14 +0200 >> From: ifat shub <shubi...@gmail.com> >> Subject: [gmx-users] Periodic Boundary Conditions g_mindist -pi >> To: gmx-users@gromacs.org >> Message-ID: >> <AANLkTi=sgjftmrf-0nvmzzogfs+xhyxv5u6ggfnhr...@mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Hi, >> >> >> >> I am running a simulation on the complex 1aik.pdb in 310K. I wanted to see >> if the complex is seeing its next periodic image, so I used the g_mindist >> command with the -pi option. My command line was: >> >> g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi >> >> The output (see below) was stable until ~344ps when there is a jump in >> the >> max internal distance (third column) from ~6nm to ~22nm. After the jump >> the >> numbers are reduced back to ~6nm and remained stable until the run is >> completed at 1ns. >> >> Does anyone know how to explain this jump? Is this a real problem or just >> a >> visualization artifact? Is there a way to avoid such jumps? >> >> >> >> Here is the mdp file I used: >> >> ------run.mdp------ >> >> integrator = md >> >> nsteps = 1000000 >> >> dt = 0.001 >> >> coulombtype = pme >> >> vdw-type = cut-off >> >> tcoupl = Berendsen >> >> tc-grps = protein non-protein >> >> tau-t = 0.1 0.1 >> >> ref-t = 310 310 >> >> nstxout = 100 >> >> nstvout = 0 >> >> nstxtcout = 100 >> >> nstenergy = 100 >> >> comm_mode = Linear ; Angular >> >> comm_grps = Protein >> >> xtc_grps = Protein >> >> energygrps = Protein >> >> ------------------ >> >> >> >> Thanks, >> >> Ifat >> >> >> >> The output: >> >> 343.7 10.813 5.924 16.445 16.445 16.445 >> >> 343.8 10.809 5.949 16.445 16.445 16.445 >> >> 343.9 10.804 5.959 16.445 16.445 16.445 >> >> 344 10.808 5.974 16.445 16.445 16.445 >> >> 344.1 0.18 21.982 16.445 16.445 16.445 >> >> 344.2 10.778 5.977 16.445 16.445 16.445 >> >> 344.3 10.768 5.996 16.445 16.445 16.445 >> >> 344.4 10.764 6.016 16.445 16.445 16.445 >> >> 344.5 10.722 6.029 16.445 16.445 16.445 >> >> 344.6 10.774 6.01 16.445 16.445 16.445 >> >> 344.7 0.174 21.984 16.445 16.445 16.445 >> >> 344.8 0.176 21.98 16.445 16.445 16.445 >> >> 344.9 0.17 22.002 16.445 16.445 16.445 >> >> 345 0.173 21.981 16.445 16.445 16.445 >> >> 345.1 0.191 21.954 16.445 16.445 16.445 >> >> 345.2 0.183 21.958 16.445 16.445 16.445 >> >> 345.3 0.181 22.012 16.445 16.445 16.445 >> >> 345.4 0.17 22.054 16.445 16.445 16.445 >> >> 345.5 0.168 22.054 16.445 16.445 16.445 >> >> 345.6 0.189 22.039 16.445 16.445 16.445 >> >> 345.7 0.171 22.007 16.445 16.445 16.445 >> >> 345.8 0.186 22.031 16.445 16.445 16.445 >> >> 345.9 0.171 22.077 16.445 16.445 16.445 >> >> 346 0.187 21.99 16.445 16.445 16.445 >> >> 346.1 0.173 21.984 16.445 16.445 16.445 >> >> 346.2 0.181 22.02 16.445 16.445 16.445 >> >> 346.3 10.82 5.984 16.445 16.445 16.445 >> >> 346.4 10.81 6.002 16.445 16.445 16.445 >> >> 346.5 10.819 6.008 16.445 16.445 16.445 >> >> 346.6 10.813 5.996 16.445 16.445 16.445 >> >> 346.7 10.781 6.006 16.445 16.445 16.445 >> >> 346.8 10.793 6.026 16.445 16.445 16.445 >> >> 346.9 10.745 5.985 16.445 16.445 16.445 >> >> 347 10.762 5.999 16.445 16.445 16.445 >> >> 347.1 10.781 5.984 16.445 16.445 16.445 >> >> 347.2 10.784 6.002 16.445 16.445 16.445 >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: >> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/8495d798/attachment-0001.html >> >> ------------------------------ >> >> Message: 5 >> Date: Wed, 16 Feb 2011 10:43:56 +0100 >> From: Tsjerk Wassenaar <tsje...@gmail.com> >> Subject: Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: >> <AANLkTinr05YyKV7rqzCSwEch=abxfur+adkenmxem...@mail.gmail.com> >> Content-Type: text/plain; charset=ISO-8859-1 >> >> Hi Ifat, >> >> I guess this is a jump over the periodic boundaries. You should remove >> jumps from the trajectory (-pbc nojump) before running g_mindist -pi. >> >> Cheers, >> >> Tsjerk >> >> On Wed, Feb 16, 2011 at 10:19 AM, ifat shub <shubi...@gmail.com> wrote: >> > Hi, >> > >> > >> > >> > I am running a simulation on the complex 1aik.pdb in 310K. I wanted to >> > see >> > if the complex is seeing its next periodic image, so I used the >> > g_mindist >> > command with the -pi option. My command line was: >> > >> > g_mindist -f run.xtc -s run.gro -n index.ndx -od tmp.xvg -pi >> > >> > The output (see below) was stable until ~344ps when there is a jump in >> > the >> > max internal distance (third column) from ~6nm to ~22nm. After the jump >> > the >> > numbers are reduced back to ~6nm and remained stable until the run is >> > completed at 1ns. >> > >> > Does anyone know how to explain this jump? Is this a real problem or >> > just a >> > visualization artifact? Is there a way to avoid such jumps? >> > >> > >> > >> > Here is the mdp file I used: >> > >> > ------run.mdp------ >> > >> > integrator = md >> > >> > nsteps = 1000000 >> > >> > dt = 0.001 >> > >> > coulombtype = pme >> > >> > vdw-type = cut-off >> > >> > tcoupl = Berendsen >> > >> > tc-grps = protein non-protein >> > >> > tau-t = 0.1 0.1 >> > >> > ref-t = 310 310 >> > >> > nstxout = 100 >> > >> > nstvout = 0 >> > >> > nstxtcout = 100 >> > >> > nstenergy = 100 >> > >> > comm_mode = Linear ; Angular >> > >> > comm_grps = Protein >> > >> > xtc_grps = Protein >> > >> > energygrps = Protein >> > >> > ------------------ >> > >> > >> > >> > Thanks, >> > >> > Ifat >> > >> > >> > >> > The output: >> > >> > 343.7 10.813 5.924 16.445 16.445 16.445 >> > >> > 343.8 10.809 5.949 16.445 16.445 16.445 >> > >> > 343.9 10.804 5.959 16.445 16.445 16.445 >> > >> > 344 10.808 5.974 16.445 16.445 16.445 >> > >> > 344.1 0.18 21.982 16.445 16.445 16.445 >> > >> > 344.2 10.778 5.977 16.445 16.445 16.445 >> > >> > 344.3 10.768 5.996 16.445 16.445 16.445 >> > >> > 344.4 10.764 6.016 16.445 16.445 16.445 >> > >> > 344.5 10.722 6.029 16.445 16.445 16.445 >> > >> > 344.6 10.774 6.01 16.445 16.445 16.445 >> > >> > 344.7 0.174 21.984 16.445 16.445 16.445 >> > >> > 344.8 0.176 21.98 16.445 16.445 16.445 >> > >> > 344.9 0.17 22.002 16.445 16.445 16.445 >> > >> > 345 0.173 21.981 16.445 16.445 16.445 >> > >> > 345.1 0.191 21.954 16.445 16.445 16.445 >> > >> > 345.2 0.183 21.958 16.445 16.445 16.445 >> > >> > 345.3 0.181 22.012 16.445 16.445 16.445 >> > >> > 345.4 0.17 22.054 16.445 16.445 16.445 >> > >> > 345.5 0.168 22.054 16.445 16.445 16.445 >> > >> > 345.6 0.189 22.039 16.445 16.445 16.445 >> > >> > 345.7 0.171 22.007 16.445 16.445 16.445 >> > >> > 345.8 0.186 22.031 16.445 16.445 16.445 >> > >> > 345.9 0.171 22.077 16.445 16.445 16.445 >> > >> > 346 0.187 21.99 16.445 16.445 16.445 >> > >> > 346.1 0.173 21.984 16.445 16.445 16.445 >> > >> > 346.2 0.181 22.02 16.445 16.445 16.445 >> > >> > 346.3 10.82 5.984 16.445 16.445 16.445 >> > >> > 346.4 10.81 6.002 16.445 16.445 16.445 >> > >> > 346.5 10.819 6.008 16.445 16.445 16.445 >> > >> > 346.6 10.813 5.996 16.445 16.445 16.445 >> > >> > 346.7 10.781 6.006 16.445 16.445 16.445 >> > >> > 346.8 10.793 6.026 16.445 16.445 16.445 >> > >> > 346.9 10.745 5.985 16.445 16.445 16.445 >> > >> > 347 10.762 5.999 16.445 16.445 16.445 >> > >> > 347.1 10.781 5.984 16.445 16.445 16.445 >> > >> > 347.2 10.784 6.002 16.445 16.445 16.445 >> > >> > >> > >> > >> > >> > -- >> > 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 >> > >> >> >> >> -- >> 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 >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >> End of gmx-users Digest, Vol 82, Issue 125 >> ****************************************** > > > > -- > 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 > -- 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 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