Re: [gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water
Hi XAvier, Thanks for your help! I will try it now. Have a great day! Wei > > Hi Wei, > > What you need here is to increase the rdd to 1.4/1.5 nm. You can do that > using the -rdd option of mdrun. > > Turning pme on would have no effect. > > XAvier. > > On Feb 8, 2011, at 20:56, wez...@ucalgary.ca wrote: > >> Dear All, >> >> I have performed a simulation of POPC with polarisable water model in >> presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for >> the >> electrostatic interactions and the job was done on a 8-core node with >> domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and >> 16000 water. However, the simulation crashed after about 100 ns. >> >> The error message is given by: >> DD step 5103999 load imb.: force 5.1% >> >> Step Time Lambda >>5104000 102080.00.0 >> >> Energies (kJ/mol) >> Bond G96AngleLJ (SR) Coulomb (SR) >> Potential >>1.18271e+046.29597e+04 -4.34519e+05 -3.22701e+05 >> -6.82433e+05 >>Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd >> () >>1.66874e+05 -5.15560e+053.10498e+021.50257e+01 >> 1.85079e-04 >> >> >> Not all bonded interactions have been properly assigned to the domain >> decomposition cells >> >> A list of missing interactions: >>G96Angle of 19936 missing 1 >> >> Molecule type 'POPC' >> the first 10 missing interactions, except for exclusions: >>G96Angle atoms456 global 3696 3697 3698 >> >> --- >> Program mdrun_s_mpi, VERSION 4.0.7 >> Source code file: domdec_top.c, line: 341 >> >> Fatal error: >> 1 of the 56736 bonded interactions could not be calculated because some >> atoms involved moved further apart than the multi-body cut-off distance >> (1 >> nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for >> pairs >> and tabulated bonds also see option -ddcheck >> >> I turned on PME for testing, but it crashed within 1 ns. Could somebody >> give me some suggestion on how to solve this problem? >> Thanks! >> >> Wei Zhao >> >> >> -- >> 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 > > > -- 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] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water
Hi Wei, What you need here is to increase the rdd to 1.4/1.5 nm. You can do that using the -rdd option of mdrun. Turning pme on would have no effect. XAvier. On Feb 8, 2011, at 20:56, wez...@ucalgary.ca wrote: > Dear All, > > I have performed a simulation of POPC with polarisable water model in > presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for the > electrostatic interactions and the job was done on a 8-core node with > domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and > 16000 water. However, the simulation crashed after about 100 ns. > > The error message is given by: > DD step 5103999 load imb.: force 5.1% > > Step Time Lambda >5104000 102080.00.0 > > Energies (kJ/mol) > Bond G96AngleLJ (SR) Coulomb (SR) Potential >1.18271e+046.29597e+04 -4.34519e+05 -3.22701e+05 -6.82433e+05 >Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd () >1.66874e+05 -5.15560e+053.10498e+021.50257e+011.85079e-04 > > > Not all bonded interactions have been properly assigned to the domain > decomposition cells > > A list of missing interactions: >G96Angle of 19936 missing 1 > > Molecule type 'POPC' > the first 10 missing interactions, except for exclusions: >G96Angle atoms456 global 3696 3697 3698 > > --- > Program mdrun_s_mpi, VERSION 4.0.7 > Source code file: domdec_top.c, line: 341 > > Fatal error: > 1 of the 56736 bonded interactions could not be calculated because some > atoms involved moved further apart than the multi-body cut-off distance (1 > nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs > and tabulated bonds also see option -ddcheck > > I turned on PME for testing, but it crashed within 1 ns. Could somebody > give me some suggestion on how to solve this problem? > Thanks! > > Wei Zhao > > > -- > 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
[gmx-users] ask for help on MARTINI SIMULATION OF POPC lipids with polarisable water
Dear All, I have performed a simulation of POPC with polarisable water model in presence of 0.2 mol CaCl2 based on MARTINI CG model. I used shift for the electrostatic interactions and the job was done on a 8-core node with domain decomposition 2 2 2. The lipid bilayer consists of 512 lipid and 16000 water. However, the simulation crashed after about 100 ns. The error message is given by: DD step 5103999 load imb.: force 5.1% Step Time Lambda 5104000 102080.00.0 Energies (kJ/mol) Bond G96AngleLJ (SR) Coulomb (SR) Potential 1.18271e+046.29597e+04 -4.34519e+05 -3.22701e+05 -6.82433e+05 Kinetic En. Total EnergyTemperature Pressure (bar) Cons. rmsd () 1.66874e+05 -5.15560e+053.10498e+021.50257e+011.85079e-04 Not all bonded interactions have been properly assigned to the domain decomposition cells A list of missing interactions: G96Angle of 19936 missing 1 Molecule type 'POPC' the first 10 missing interactions, except for exclusions: G96Angle atoms456 global 3696 3697 3698 --- Program mdrun_s_mpi, VERSION 4.0.7 Source code file: domdec_top.c, line: 341 Fatal error: 1 of the 56736 bonded interactions could not be calculated because some atoms involved moved further apart than the multi-body cut-off distance (1 nm) or the two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated bonds also see option -ddcheck I turned on PME for testing, but it crashed within 1 ns. Could somebody give me some suggestion on how to solve this problem? Thanks! Wei Zhao -- 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
