Re: [gmx-users] Periodic Boundary Conditions g_mindist -pi
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 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 = 100 > > 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 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] Periodic Boundary Conditions g_mindist -pi
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 = 100 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 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] Periodic Boundary Conditions & Location of Atoms Near Box Edges
Hi Darrell, No, you just have to make sure that the bond lengths are correct in the periodic system. The PBC are invariant under translation. Cheers, Tsjerk On 9/17/09, Darrell Koskinen wrote: > Dear GROMACS Gurus, > In order to correctly model an infinite graphene sheet using periodic > boundary conditions, should the box edges be located at the midpoints > between the atomic bonds? > > Thanks. > > Darrell > ___ > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Periodic Boundary Conditions & Location of Atoms Near Box Edges
Dear GROMACS Gurus, In order to correctly model an infinite graphene sheet using periodic boundary conditions, should the box edges be located at the midpoints between the atomic bonds? Thanks. Darrell ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
RE: [gmx-users] periodic boundary conditions in g_rdf
Hi Berk, thanks for the answearing. Here is my command line: g_rdf -f file.xtc -s file.tpr -n index.ndx -com -rdf mol_com -xy then i select 'Protein' as reference group and 'upper-leaf_&_P8' (just the P8 atoms from the upper-leaflet) in the 1 group option. The value of the g_rdf at the half of the box is roughly 0.5 - 0.6 In the attachment is de g(r) that i got. Thanks in advance! From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Subject: RE: [gmx-users] periodic boundary conditions in g_rdf Date: Mon, 3 Nov 2008 10:20:08 +0100 Hi, To what value does your rdf go then? You have pbc in your system, so running with -nopbc is incorrect. The rdf will then stop at half the box, since you molecules are in the box and your peptide is probably in the middle, leading to a longest distance of roughly half the box. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 31 Oct 2008 16:55:54 -0600 Subject: [gmx-users] periodic boundary conditions in g_rdf Hi everybody. I'm working a system with a peptide embedded in a lipid bilayer and I try to get the two-dimentional g_rdf for the upper leaflet around the peptide with the -xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a used -nopbc i get almost the same result (just multiplied by a constant) and the RDF is always cutted at the half of size of the box. Any help will be appreciated. Thanks in advance. Conoce el perfil completo de todos tus amigos de Windows Live Messenger justo aquí: Windows Live Spaces Express yourself instantly with MSN Messenger! MSN Messenger _ Live Search premia tus búsquedas, llévate hasta ¡Un Auto! http://www.ganabuscando.com/Default.aspx<>___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] periodic boundary conditions in g_rdf
Hi, To what value does your rdf go then? You have pbc in your system, so running with -nopbc is incorrect. The rdf will then stop at half the box, since you molecules are in the box and your peptide is probably in the middle, leading to a longest distance of roughly half the box. Berk From: [EMAIL PROTECTED] To: gmx-users@gromacs.org Date: Fri, 31 Oct 2008 16:55:54 -0600 Subject: [gmx-users] periodic boundary conditions in g_rdf Hi everybody. I'm working a system with a peptide embedded in a lipid bilayer and I try to get the two-dimentional g_rdf for the upper leaflet around the peptide with the -xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a used -nopbc i get almost the same result (just multiplied by a constant) and the RDF is always cutted at the half of size of the box. Any help will be appreciated. Thanks in advance. Conoce el perfil completo de todos tus amigos de Windows Live Messenger justo aquí: Windows Live Spaces _ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] periodic boundary conditions in g_rdf
Hi everybody. I'm working a system with a peptide embedded in a lipid bilayer and I try to get the two-dimentional g_rdf for the upper leaflet around the peptide with the -xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a used -nopbc i get almost the same result (just multiplied by a constant) and the RDF is always cutted at the half of size of the box. Any help will be appreciated. Thanks in advance. _ Live Search premia tus búsquedas, llévate hasta ¡Un Auto! http://www.ganabuscando.com/Default.aspx___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Periodic Boundary conditions
The problem is the combination of pbc=full and comm_mode = angular. With pbc=xyz it will work. We will add a check for this. Anyhow, pbc=full is only useful when you have periodic molecules. Berk. From: "Paul Whitford" <[EMAIL PROTECTED]> Reply-To: Discussion list for GROMACS users To: "gmx-users@gromacs.org" Subject: [gmx-users] Periodic Boundary conditions Date: Wed, 7 Nov 2007 16:41:48 -0800 I am running v3.3.2. I am running an RNA strand with a homemade potential. When I run a single molecule in a periodic box, the system is fine until one nucleic acid crosses the boundary. THen the entire nucleic acid gets moved to the opposite side of the box. Since there are bonds this results in an exploding system. I am running on 4 processors and am using the following mdp file. Any ideas what is going on? The system runs normally for over 20 time steps. It runs fine until the boundary issue occurs. title= Paul Template ;Preprocessor cpp = cpp ;Run control: A leap-frog algorithm for integrating Newton's equations. integrator = sd :time step in femtoseconds dt = 0.0005 ;number of stepsi nsteps = 1000 ;frequency to write coordinates to output trajectory file nstxout = 0 ;frequency to write velocities to output trajectory file nstvout = 0 ;frequency to write energies to log file nstlog = 1000 ;frequency to write energies to energy file nstenergy= 1000 ;frequency to write coordinates to xtc trajectory nstxtcout= 1000 ;group(s) to write to xtc trajectory xtc_grps = system ;group(s) to write to energy file energygrps = system ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 50 coulombtype = Cut-off ;Make a grid in the box and only check atoms in neighboring grid cells ;when constructing a new neighbor list every nstlist steps. ns_type = grid ;cut-off distance for the short-range neighbor list rlist= 2.5 ;treatment of electrostatic interactions table_extension = 150.0 rcoulomb = 2.5 epsilon_r= 0 ;treatment of van der waals interactions rvdw = 2.5 ; Periodic boudary conditions in all the directions pbc = full ;Temperature coupling tc-grps = system tau_t= 10.0 ref_t= 100 ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 100 gen_seed = 12345 ;Constrain all bonds constraints = none ;constraint_algorithm= lincs ;lincs_iter=8 comm_mode = angular thanks -Paul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Periodic Boundary conditions
I am running v3.3.2. I am running an RNA strand with a homemade potential. When I run a single molecule in a periodic box, the system is fine until one nucleic acid crosses the boundary. THen the entire nucleic acid gets moved to the opposite side of the box. Since there are bonds this results in an exploding system. I am running on 4 processors and am using the following mdp file. Any ideas what is going on? The system runs normally for over 20 time steps. It runs fine until the boundary issue occurs. title= Paul Template ;Preprocessor cpp = cpp ;Run control: A leap-frog algorithm for integrating Newton's equations. integrator = sd :time step in femtoseconds dt = 0.0005 ;number of stepsi nsteps = 1000 ;frequency to write coordinates to output trajectory file nstxout = 0 ;frequency to write velocities to output trajectory file nstvout = 0 ;frequency to write energies to log file nstlog = 1000 ;frequency to write energies to energy file nstenergy= 1000 ;frequency to write coordinates to xtc trajectory nstxtcout= 1000 ;group(s) to write to xtc trajectory xtc_grps = system ;group(s) to write to energy file energygrps = system ;Frequency to update the neighbor list (and the long-range forces, ;when using twin-range cut-off's). nstlist = 50 coulombtype = Cut-off ;Make a grid in the box and only check atoms in neighboring grid cells ;when constructing a new neighbor list every nstlist steps. ns_type = grid ;cut-off distance for the short-range neighbor list rlist= 2.5 ;treatment of electrostatic interactions table_extension = 150.0 rcoulomb = 2.5 epsilon_r= 0 ;treatment of van der waals interactions rvdw = 2.5 ; Periodic boudary conditions in all the directions pbc = full ;Temperature coupling tc-grps = system tau_t= 10.0 ref_t= 100 ;Pressure coupling Pcoupl = no ;Velocity generation gen_vel = yes gen_temp = 100 gen_seed = 12345 ;Constrain all bonds constraints = none ;constraint_algorithm= lincs ;lincs_iter=8 comm_mode = angular thanks -Paul ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
