Re: [gmx-users] Minimum distance between periodic images
Thank you sir. On Tue, Oct 22, 2013 at 2:48 PM, Tsjerk Wassenaar wrote: > Hi Nidhi, > > These are periodicity artifacts. Make sure that you remove jumps over PBC > from your trajectory by using trjconv -pbc nojump. > > Cheers, > > Tsjerk > > > On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal >wrote: > > > Dear all users > > > > I have simulated a protein with two chains (153 residues each) for > > 50ns(restarting crashed run 3 times) using a cubic box with each side as > > 11nm. After finding the closest distance between the periodic images, I > > found that the closest distance becomes lesser than 1 after 23ns for few > > ns and then again shoots up (and fluctuates around the previous value) > and > > then again becomes lesser than 1 around 49ns.The command which I used: > > g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od > > mindist.xvg > > -pi > > > > Similar trend is seen when I plotted rmsd curve and distance between the > > two chains or any other analysis curve (ie at those specific time > intervals > > in between, the value shoots up) > > > > My question is : Will it be reasonable enough to carry out my analysis > for > > first 22ns and discard the rest? Is this the problem due to smaller box > > size or some other parameter as the previous studies (through literature > > survey) have used even much lesser box length (although their simulations > > were also of short duration than 50ns). > > > > I have posted the output of minimum distance between periodic images at : > > > > > https://plus.google.com/photos/109332801667278171972/albums/5937501788329595121?authkey=CJHD-9XO7dH4jgE > > and rmsd wrt c alpha at : > > > > > > > https://plus.google.com/photos/109332801667278171972/albums/5937501062407227393?authkey=CKOE9sP5pMO2NA > > > > Please help me figure out the problem. > > Thanks in advance. > > -- > > gmx-users mailing listgmx-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. > -- > gmx-users mailing listgmx-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 listgmx-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
Re: [gmx-users] Minimum distance between periodic images
Hi Nidhi, These are periodicity artifacts. Make sure that you remove jumps over PBC from your trajectory by using trjconv -pbc nojump. Cheers, Tsjerk On Tue, Oct 22, 2013 at 11:14 AM, Nidhi Katyal wrote: > Dear all users > > I have simulated a protein with two chains (153 residues each) for > 50ns(restarting crashed run 3 times) using a cubic box with each side as > 11nm. After finding the closest distance between the periodic images, I > found that the closest distance becomes lesser than 1 after 23ns for few > ns and then again shoots up (and fluctuates around the previous value) and > then again becomes lesser than 1 around 49ns.The command which I used: > g_mindist -f md-run-1-noPBC.xtc -s md-run-1.tpr -n index.ndx -od > mindist.xvg > -pi > > Similar trend is seen when I plotted rmsd curve and distance between the > two chains or any other analysis curve (ie at those specific time intervals > in between, the value shoots up) > > My question is : Will it be reasonable enough to carry out my analysis for > first 22ns and discard the rest? Is this the problem due to smaller box > size or some other parameter as the previous studies (through literature > survey) have used even much lesser box length (although their simulations > were also of short duration than 50ns). > > I have posted the output of minimum distance between periodic images at : > > https://plus.google.com/photos/109332801667278171972/albums/5937501788329595121?authkey=CJHD-9XO7dH4jgE > and rmsd wrt c alpha at : > > > https://plus.google.com/photos/109332801667278171972/albums/5937501062407227393?authkey=CKOE9sP5pMO2NA > > Please help me figure out the problem. > Thanks in advance. > -- > gmx-users mailing listgmx-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. -- gmx-users mailing listgmx-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
Re: [gmx-users] minimum distance between periodic images does not aggree with box dimensions
Hi Thomas, The rhombic dodecahedron is built as a rectangular brick, which makes it easy to fill with a rectangular bricklet of water. Now, for the smaller distances the short edge of the rectangular brick is smaller than the diameter of the particle, and it is represented fragmented. Best way to get acquainted with this stuff is drawing a circle, and a hexagon around it. Then tesselate a patch of space and draw the corresponding rectangular cell. Try to translate the rectangle such that the whole circle fits in. Good luck! :p For the other thing, notice that the distance reported is close to a bond length. Before checking the distances between periodic images, make sure that the solute not fragmented... Cheers, Tsjerk On Mon, Apr 30, 2012 at 4:38 PM, Thomas Evangelidis wrote: > > Dear GROMACS users, > > I have a nanoparticle (perfect sphere) and want to enclose it into a rhombic > dodecahedron. For this purpose I use the following command lines > > editconf_d4.5.5 -f nano.gro -bt dodecahedron -d 1 -c -o nano_box.gro > grompp_d4.5.5 -f em.mdp -c nano_box.gro -p nano.top -o nano_box_EM.tpr > mdrun_d4.5.5 -v -deffnm nano_box_EM > > echo 0 | trjconv_d4.5.5 -pbc mol -ur compact -f nano_box_EM.trr -s > nano_box_EM.tpr -o nano_em_dodecahedron.xtc > echo 2 | g_mindist_d4.5.5 -f nano_em_dodecahedron.xtc -s nano_box_EM.tpr -pi > -od nano_mindist.xvg > > The first paradox is that the nanoparticle is fragmented in the dodecahedron > representation for -d (editconf option) less that 1 nm. The second paradox > is that the minimum distance between periodic images for -d 0.5, 1, 2, 3 is > 0.183, 0.237, 4.171 and 6.167 nm respectively. The last two distances are > close to the expected values but the first two are far from them. I would > expect ~1 and ~2 nm for -d 0.5 and 1 respectively, since by definition with > option -d and dodecahedron, the dimensions are set to the diameter of the > system (largest distance between atoms) plus twice the specified distance. > Can anyone explain what's happening? > > Thanks in advance. > Thomas > > > > -- > > == > > Thomas Evangelidis > > PhD student > > Biomedical Research Foundation, Academy of Athens > > 4 Soranou Ephessiou , 115 27 Athens, Greece > > email: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > > > > > -- > 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 listgmx-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
