Re: [gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
On Aug 16, 2010, at 1:33 PM, Anirban Ghosh wrote: Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option with mdrun, right? yes And why does this curvature of the membrane occurs? No idea! Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole wrote: Although a bit worrying the curvature of your bilayer is not responsible for the error message you are seeing. to solve the problem you have to increase to use the -rrd option (see manual for explanation). Typicaly a value of 1.4 to 1.6 should be fine. On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote: Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih. LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total Energy Temperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+05 3.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Regards, Anirban -- 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 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 thewww interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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 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] Not all bonded interactions have been properly assigned to the domain decomposition cells
Anirban Ghosh wrote: Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih.LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total EnergyTemperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Search the list archive. This error has come up before, and I know there's been at least one instance of it for a CG system. I believe the answer was to increase -rdd (since bonded interactions occur at longer distance in CG systems), but please do the search for yourself. -Justin Regards, Anirban -- 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 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] Not all bonded interactions have been properly assigned to the domain decomposition cells
Thanks a lot XAvier for clarifying my doubt. You mean to say "-rdd" option with mdrun, right? And why does this curvature of the membrane occurs? Thanks a lot once again. Regards, Anirban On Mon, Aug 16, 2010 at 3:53 PM, XAvier Periole wrote: > > Although a bit worrying the curvature of your bilayer is not > responsible for the error message you are seeing. > > to solve the problem you have to increase to use the -rrd option > (see manual for explanation). Typicaly a value of 1.4 to 1.6 should > be fine. > > > On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote: > > Hi ALL, >> >> I have made a CGMD system with multiple copies of a single protein in >> bilayer, by replicating the monomer using genconf in the X-Y plane. After >> running CGMD for about 100 ns, I am getting the following error: >> >> >> >> Energies (kJ/mol) >> Bond G96AngleProper Dih. Improper Dih.LJ (SR) >>4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 >> Coulomb (SR) PotentialKinetic En. Total EnergyTemperature >> -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 >> Pressure (bar) Cons. rmsd () >> -9.97540e+001.69233e-05 >> >> >> Not all bonded interactions have been properly assigned to the domain >> decomposition cells >> >> A list of missing interactions: >>G96Angle of 28064 missing 1 >> >> Molecule type 'DSPC' >> the first 10 missing interactions, except for exclusions: >>G96Angle atoms 10 11 12 global 5309 5310 5311 >> >> --- >> Program mdrun_mpi, VERSION 4.0.7 >> Source code file: domdec_top.c, line: 341 >> >> Fatal error: >> 1 of the 62352 bonded interactions could not be calculated because some >> atoms involved moved further apart than the multi-body cut-off distance (1.2 >> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs >> and tabulated bonds also see option -ddcheck >> >> >> >> On visual inspection I found that the bilayer is becoming curved (image >> attached). In the .top file I have mentioned the different monomers of my >> system as: >> >> >> -- >> [ system ] >> PROT in DSPC Bilayer >> >> [ molecules ] >> Protein 1 >> DSPC104 >> W 1397 >> NA+ 0 >> CL- 4 >> Protein 1 >> DSPC104 >> W 1397 >> NA+0 >> CL- 4 >> >> - >> >> How can I resolve this error? Any suggestion is welcome. >> >> Regards, >> >> Anirban >> -- >> 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 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 thewww interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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] Not all bonded interactions have been properly assigned to the domain decomposition cells
Although a bit worrying the curvature of your bilayer is not responsible for the error message you are seeing. to solve the problem you have to increase to use the -rrd option (see manual for explanation). Typicaly a value of 1.4 to 1.6 should be fine. On Aug 16, 2010, at 12:16 PM, Anirban Ghosh wrote: Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih. LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total Energy Temperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+05 3.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Regards, Anirban -- 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 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] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi ALL, I have made a CGMD system with multiple copies of a single protein in bilayer, by replicating the monomer using genconf in the X-Y plane. After running CGMD for about 100 ns, I am getting the following error: Energies (kJ/mol) Bond G96AngleProper Dih. Improper Dih.LJ (SR) 4.73694e+043.00928e+044.68451e+038.26028e+02 -1.29727e+06 Coulomb (SR) PotentialKinetic En. Total EnergyTemperature -7.97216e+03 -1.7e+062.24656e+05 -9.97613e+053.21675e+02 Pressure (bar) Cons. rmsd () -9.97540e+001.69233e-05 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 28064 missing 1 Molecule type 'DSPC' the first 10 missing interactions, except for exclusions: G96Angle atoms 10 11 12 global 5309 5310 5311 --- Program mdrun_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 62352 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1.2 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck On visual inspection I found that the bilayer is becoming curved (image attached). In the .top file I have mentioned the different monomers of my system as: -- [ system ] PROT in DSPC Bilayer [ molecules ] Protein 1 DSPC104 W 1397 NA+ 0 CL- 4 Protein 1 DSPC104 W 1397 NA+0 CL- 4 - How can I resolve this error? Any suggestion is welcome. Regards, Anirban <>-- 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] Not all bonded interactions have been properly assigned to the domain decomposition cells
Jennifer Williams wrote: Hi , I am getting the following error when I try to run in parallel (I've tried with 8 and 2 nodes and get the same). Not all bonded interactions have been properly assigned to the domain decomposition cells But my simulation works when I run in serial. I'm using gromacs 4.0.5. I am working on a mesoprous silica which I define as a single residue (each atom is assigned to a single charge group). How many atoms in what size simulation cell? What are your v-sites? I've tried changing table_ext in the .mdp file (I first increased it to 2.5 and then 30) following advice on previous forum posts but I still get the same thing. Does anyone know why this is happening and how I can fix this? I could run in serial but it would take too long. I also get a NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Is this part of the same problem or a different thing altogether? My random guess is that there's a single problem with the interaction of parallel DD, PBC, vsites, periodic molecules and/or constraints. Berk did fix a bug earlier this month whose git commit description is "fixed v-site pbc bug with charge groups consisting ofonly multiple v-sites" but I do not know if this is at all applicable. Compiling the git release-4-0-patches branch and trying to run with that may help. See bottom of text also. I've pasted my md.log file below Thanks 010/AP_ready> more md.log Log file opened on Tue Oct 27 13:31:44 2009 Host: vlxbig20.see.ed.ac.uk pid: 6930 nodeid: 0 nnodes: 8 The Gromacs distribution was built Tue Jul 21 13:18:34 BST 2009 by parameters of the run: integrator = md nsteps = 500 init_step= 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 0 comm_mode= None nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstenergy= 1000 nstxtcout= 1000 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 39 nky = 39 nkz = 64 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bPeriodicMols= TRUE bContinuation= FALSE bShakeSOR= FALSE etc = Nose-Hoover epc = No epctype = Isotropic tau_p= 1 ref_p (3x3): ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00} ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00} ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00} compress (3x3): compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00} compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00} compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00} refcoord_scaling = No posres_com (3): posres_com[0]= 0.0e+00 posres_com[1]= 0.0e+00 posres_com[2]= 0.0e+00 posres_comB (3): posres_comB[0]= 0.0e+00 posres_comB[1]= 0.0e+00 posres_comB[2]= 0.0e+00 andersen_seed= 815131 rlist= 1.5 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.5 vdwtype = Shift rvdw_switch = 1.2 rvdw = 1.5 epsilon_r= 1 epsilon_rf = 1 tabext = 2.5 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = EnerPres free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 nwall= 0 wall_type= 9-3 wall_atomtype[0] = -1 wall_atomtype[1] = -1 wall_density[0] = 0 wall_density[1] = 0 wall_ewald_zfac = 3 pull = no disre= No disre_weighting = Conservative disre_mixed = FALSE dr_fc= 1000 dr_tau = 0 nstdisreout = 100 orires_fc= 0 orires_tau = 0 nstorireout = 100 dihre-fc = 1000 em_stepsize = 0.01 em_tol = 10 niter= 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr= 10 ConstAlg = Lin
[gmx-users] Not all bonded interactions have been properly assigned to the domain decomposition cells
Hi , I am getting the following error when I try to run in parallel (I've tried with 8 and 2 nodes and get the same). Not all bonded interactions have been properly assigned to the domain decomposition cells But my simulation works when I run in serial. I'm using gromacs 4.0.5. I am working on a mesoprous silica which I define as a single residue (each atom is assigned to a single charge group). I've tried changing table_ext in the .mdp file (I first increased it to 2.5 and then 30) following advice on previous forum posts but I still get the same thing. Does anyone know why this is happening and how I can fix this? I could run in serial but it would take too long. I also get a NOTE: Periodic molecules: can not easily determine the required minimum bonded cut-off, using half the non-bonded cut-off Is this part of the same problem or a different thing altogether? I've pasted my md.log file below Thanks 010/AP_ready> more md.log Log file opened on Tue Oct 27 13:31:44 2009 Host: vlxbig20.see.ed.ac.uk pid: 6930 nodeid: 0 nnodes: 8 The Gromacs distribution was built Tue Jul 21 13:18:34 BST 2009 by parameters of the run: integrator = md nsteps = 500 init_step= 0 ns_type = Grid nstlist = 10 ndelta = 2 nstcomm = 0 comm_mode= None nstlog = 1000 nstxout = 1000 nstvout = 1000 nstfout = 1000 nstenergy= 1000 nstxtcout= 1000 init_t = 0 delta_t = 0.001 xtcprec = 1000 nkx = 39 nky = 39 nkz = 64 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 0 epsilon_surface = 0 optimize_fft = TRUE ePBC = xyz bPeriodicMols= TRUE bContinuation= FALSE bShakeSOR= FALSE etc = Nose-Hoover epc = No epctype = Isotropic tau_p= 1 ref_p (3x3): ref_p[0]={ 0.0e+00, 0.0e+00, 0.0e+00} ref_p[1]={ 0.0e+00, 0.0e+00, 0.0e+00} ref_p[2]={ 0.0e+00, 0.0e+00, 0.0e+00} compress (3x3): compress[0]={ 0.0e+00, 0.0e+00, 0.0e+00} compress[1]={ 0.0e+00, 0.0e+00, 0.0e+00} compress[2]={ 0.0e+00, 0.0e+00, 0.0e+00} refcoord_scaling = No posres_com (3): posres_com[0]= 0.0e+00 posres_com[1]= 0.0e+00 posres_com[2]= 0.0e+00 posres_comB (3): posres_comB[0]= 0.0e+00 posres_comB[1]= 0.0e+00 posres_comB[2]= 0.0e+00 andersen_seed= 815131 rlist= 1.5 rtpi = 0.05 coulombtype = PME rcoulomb_switch = 0 rcoulomb = 1.5 vdwtype = Shift rvdw_switch = 1.2 rvdw = 1.5 epsilon_r= 1 epsilon_rf = 1 tabext = 2.5 implicit_solvent = No gb_algorithm = Still gb_epsilon_solvent = 80 nstgbradii = 1 rgbradii = 2 gb_saltconc = 0 gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 sa_surface_tension = 2.092 DispCorr = EnerPres free_energy = no init_lambda = 0 sc_alpha = 0 sc_power = 0 sc_sigma = 0.3 delta_lambda = 0 nwall= 0 wall_type= 9-3 wall_atomtype[0] = -1 wall_atomtype[1] = -1 wall_density[0] = 0 wall_density[1] = 0 wall_ewald_zfac = 3 pull = no disre= No disre_weighting = Conservative disre_mixed = FALSE dr_fc= 1000 dr_tau = 0 nstdisreout = 100 orires_fc= 0 orires_tau = 0 nstorireout = 100 dihre-fc = 1000 em_stepsize = 0.01 em_tol = 10 niter= 20 fc_stepsize = 0 nstcgsteep = 1000 nbfgscorr= 10 ConstAlg = Lincs shake_tol= 0.0001 lincs_order = 4 lincs_warnangle = 30 lincs_iter = 1 bd_fric = 0 ld_seed = 1993 cos_accel= 0 deform (3x3): deform[0]={ 0.0e+00, 0.0e+00, 0.0e+00} deform[1]={ 0.0e+00, 0.0e+00, 0.0e+00} deform[2]={ 0.0e+00, 0.0e+00, 0.0e+00} userint1 = 0 userint2 = 0 userint3 = 0 userint4 = 0 user