[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 attachment: sim.jpeg-- 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 sim.jpeg-- 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
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 x.peri...@rug.nl 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 sim.jpeg-- 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
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
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 x.peri...@rug.nl 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 sim.jpeg-- 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
[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
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 = Lincs
