Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
Hi, Mark, Thanks for the reply. As suggested, I tried a water in vacuum case. Initially the water droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the simulation box. Everywhere else is just vacuum. The simulation box size is 8nm by 8nm by 8nm. SPC/E model is used to describe interaction between water molecules. Such system is first equilibrated with steep option. The mdrun simulation goes with no problem with parallel running on 32 cpus, even though there are occasionaly one or two water molecules move very fast (Mean square displacement being 200 times fast than bulk water) in the vacuum. When I switch to 64 cpus, the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group appears. Below is the parameter file I'm using. integrator = md tinit= 0 dt = 0.002 nsteps = 500 comm-mode= Linear nstcomm = 1 comm-grps= energygrps = nstlist = 1 ns_type = grid pbc = xyz rlist= 1.5 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 epsilon-r= 1 vdw-type = Cut-off ;Switch rvdw-switch = 1.0 rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Tcoupl = nose-hoover tc-grps = System tau_t= 1.0 ref_t= 300 Pcoupl = no ;Parrinello-Rahman ;no ;berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 2008 constraints = none constraint-algorithm = Lincs Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-warnangle = 30 energygrp_excl = Is there any parameters configuration wrong with the simulation? Or is there any way to go around this error? Any tip is appreciated. Thank you. Best, Yanbin -- Message: 1 Date: Thu, 02 Dec 2010 17:24:18 +1100 From: Mark Abraham mark.abra...@anu.edu.au Subject: Re: [gmx-users] How to suppress the error X particles communicatedto PME node Y are more than a cell length out of the domain decomposition cell of their charge group To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 4cf73b92.40...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/12/2010 4:16 PM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group . I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. I doubt the simulation is OK. This error message is one of several that can happen when the system is not well-enough conditioned for the MD to be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up. Here, you have atoms moving much faster than GROMACS was engineered to expect. You should be confident that a water drop in a vacuum, and your graphite surface are both stable on their own before you try the wetting simulation. For this situation, is there a way of suppressing this error? Or what else can I do? Work out why it's poorly conditioned. Mark -- 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?
Re: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
On 27/12/2010 9:22 AM, WU Yanbin wrote: Hi, Mark, Thanks for the reply. As suggested, I tried a water in vacuum case. Initially the water droplet is a cubic 4nm-by-4nm-by-4nm water box, located in the middle of the simulation box. Everywhere else is just vacuum. The simulation box size is 8nm by 8nm by 8nm. SPC/E model is used to describe interaction between water molecules. Such system is first equilibrated with steep option. The mdrun simulation goes with no problem with parallel running on 32 cpus, even though there are occasionaly one or two water molecules move very fast (Mean square displacement being 200 times fast than bulk water) in the vacuum. OK, that sounds like behaviour that might be expected... some molecules evaporate. Check the trajectory to be confident this is the situation. When I switch to 64 cpus, the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group appears. The most plausible reason for this is that the above evaporated molecules are moving so fast that they're doing what the error message says - travelling more than width of a box in one integration step. The DD implementation is predicated on that being impossible. You might succeed by arranging for the largest possible internal DD cell diameter, i.e. a 4x4x4 DD. mdrun -npme 0 might choose this, otherwise use the hidden options to mdrun (use mdrun -hidden) to use that DD with -npme 0. Otherwise, you'll need to accept the fact that there are engineering constraints on efficient parallelization algorithms, and not every situation can be catered for. For example, a simulation of a bulk LJ fluid would fail if you used so many processors that the cell diameter was too small with respect to the distribution of particle speeds. Mark Below is the parameter file I'm using. integrator = md tinit= 0 dt = 0.002 nsteps = 500 comm-mode= Linear nstcomm = 1 comm-grps= energygrps = nstlist = 1 ns_type = grid pbc = xyz rlist= 1.5 coulombtype = PME rcoulomb-switch = 0 rcoulomb = 1.5 epsilon-r= 1 vdw-type = Cut-off ;Switch rvdw-switch = 1.0 rvdw = 1.5 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no Tcoupl = nose-hoover tc-grps = System tau_t= 1.0 ref_t= 300 Pcoupl = no ;Parrinello-Rahman ;no ;berendsen Pcoupltype = isotropic tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 gen_vel = no gen_temp = 300 gen_seed = 2008 constraints = none constraint-algorithm = Lincs Shake-SOR= no shake-tol= 1e-04 lincs-order = 4 lincs-warnangle = 30 energygrp_excl = Is there any parameters configuration wrong with the simulation? Or is there any way to go around this error? Any tip is appreciated. Thank you. Best, Yanbin -- Message: 1 Date: Thu, 02 Dec 2010 17:24:18 +1100 From: Mark Abraham mark.abra...@anu.edu.au mailto:mark.abra...@anu.edu.au Subject: Re: [gmx-users] How to suppress the error X particles communicatedto PME node Y are more than a cell length out of the domain decomposition cell of their charge group To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: 4cf73b92.40...@anu.edu.au mailto:4cf73b92.40...@anu.edu.au Content-Type: text/plain; charset=ISO-8859-1; format=flowed On 2/12/2010 4:16 PM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below
Antw: [gmx-users] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
Hello, Have you also tried this simulation with a velocity rescaling thermostat in the equilibration period? Could it be that it then would work better? Bests, Emanuel WU Yanbin 02.12.10 6.16 Uhr Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group. I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. For this situation, is there a way of suppressing this error? Or what else can I do? PS: the GROMACS version I'm using is GROMACS4.5. Thank you. Best, Yanbin -- 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] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
On Dec 2, 2010, at 6:16 AM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group. I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. For this situation, is there a way of suppressing this error? Or what else can I do? If the system is small enough, you can run it on a single core and the problem cannot occur. You could also try to use particle decomposition (-pd) instead of domain decomposition. Or use less domains, i.e. less cores in total or at least less PP nodes if you use PME/PP splitting. This will at least reduce the probability for the problem to occur. Carsten PS: the GROMACS version I'm using is GROMACS4.5. Thank you. Best, Yanbin -- 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Am Fassberg 11, 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne -- 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] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group . I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. For this situation, is there a way of suppressing this error? Or what else can I do? PS: the GROMACS version I'm using is GROMACS4.5. Thank you. Best, Yanbin -- 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] How to suppress the error X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group
On 2/12/2010 4:16 PM, WU Yanbin wrote: Dear GMXers, I'm running a simulation of water contact angle measurement on top of graphite surface. Initially a water cubic box is placed on two-layer graphite surface with the rest of the box being vacuum. The water droplet is relaxed during the simulation to develop a spherical shape. An error of X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group was encountered. And I have read the suggested solutions at the link below http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group. I guess the reason for this error in my case is because of the vacuum such that the water molecules at the boundary of the droplet can move fast. I have check the trajectory and the simulation is OK. I doubt the simulation is OK. This error message is one of several that can happen when the system is not well-enough conditioned for the MD to be stable. See www.gromacs.org/Documentation/Terminology/Blowing_Up. Here, you have atoms moving much faster than GROMACS was engineered to expect. You should be confident that a water drop in a vacuum, and your graphite surface are both stable on their own before you try the wetting simulation. For this situation, is there a way of suppressing this error? Or what else can I do? Work out why it's poorly conditioned. Mark -- 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
