- Posts: 2
Vesicle simulation crashed with dry martini force
- lsloneil
-
Topic Author
- Offline
- Fresh Boarder
Less
More
8 years 3 months ago #5360
by lsloneil
Vesicle simulation crashed with dry martini force was created by lsloneil
Hi,
I'm trying to simulate a large lipid vesicle ( ~ 100 nm in diameter) with the dry martini force field. The system consists of about 1.4 million particles. I'm trying to equilibrate the system in NVT ensemble in a simulation box with length 120 nm, using the timestep of 10 fs. The simulation was running on 144 cores (6 nodes with 24 cores in each node). Below is my .mdp input file.
define = -DPOSRES -DPOSRES_FC=1000 -DBILAYER_LIPIDHEAD_FC=200
integrator = sd
tinit = 0.0
dt = 0.01
nsteps = 8000000
nstxout = 100000
nstvout = 10000
nstfout = 10000
nstlog = 10
nstenergy = 10000
nstxtcout = 1000
xtc_precision = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
epsilon_r = 15
coulombtype = Shift
rcoulomb = 1.2
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tc-grps = system
tau_t = 4.0
ref_t = 295
; Pressure coupling:
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN:
;gen_vel = yes
;gen_temp = 295
;gen_seed = 1452274742
refcoord_scaling = all
cutoff-scheme = group
The simulation crashed with the following error message.
Step 6105820:
Atom 164932 moved more than the distance allowed by the domain decomposition (4.000000) in direction Z
distance out of cell 127480.656250
Old coordinates: 38.785 21.966 103.077
New coordinates: -477239.938 16192.882 127588.617
Old cell boundaries in direction Z: 60.580 107.937
New cell boundaries in direction Z: 60.632 107.958
Program mdrun_mpi, VERSION 5.0.4
Source code file: /scratch/build/git/chemistry-roll/BUILD/sdsc-gromacs-5.0.4/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 4390
Fatal error:
An atom moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
Error on rank 58, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 58 out of 144
gcq#25: "This Puke Stinks Like Beer" (LIVE)
[cli_58]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 58
I think my simulation crashed possibly due to the large load imbalance generated by the domain decomposition. My system (lipid vesicle with implicit solvent) is highly inhomogeneous, therefore the domain decomposition algorithm will generate highly inhomogeneous domains with some domains empty and some full of particles. I tried to run the simulation with less CPUs (96 cores) and smaller timestep (1 fs) and there wasn't any problem for over 6 million steps.
However, I would still like to use more cores and large timestep to equilibrate my system. Is there any better way to control the load balance and domain decomposition such that I could equilibrate the system more efficiently? The dry martini paper said for such kind of vesicle simulations domain decomposition scheme should be chosen carefully. Is there a guidance for doing so?
Thanks very much.
I'm trying to simulate a large lipid vesicle ( ~ 100 nm in diameter) with the dry martini force field. The system consists of about 1.4 million particles. I'm trying to equilibrate the system in NVT ensemble in a simulation box with length 120 nm, using the timestep of 10 fs. The simulation was running on 144 cores (6 nodes with 24 cores in each node). Below is my .mdp input file.
define = -DPOSRES -DPOSRES_FC=1000 -DBILAYER_LIPIDHEAD_FC=200
integrator = sd
tinit = 0.0
dt = 0.01
nsteps = 8000000
nstxout = 100000
nstvout = 10000
nstfout = 10000
nstlog = 10
nstenergy = 10000
nstxtcout = 1000
xtc_precision = 100
nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4
epsilon_r = 15
coulombtype = Shift
rcoulomb = 1.2
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No
tc-grps = system
tau_t = 4.0
ref_t = 295
; Pressure coupling:
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN:
;gen_vel = yes
;gen_temp = 295
;gen_seed = 1452274742
refcoord_scaling = all
cutoff-scheme = group
The simulation crashed with the following error message.
Step 6105820:
Atom 164932 moved more than the distance allowed by the domain decomposition (4.000000) in direction Z
distance out of cell 127480.656250
Old coordinates: 38.785 21.966 103.077
New coordinates: -477239.938 16192.882 127588.617
Old cell boundaries in direction Z: 60.580 107.937
New cell boundaries in direction Z: 60.632 107.958
Program mdrun_mpi, VERSION 5.0.4
Source code file: /scratch/build/git/chemistry-roll/BUILD/sdsc-gromacs-5.0.4/gromacs-5.0.4/src/gromacs/mdlib/domdec.c, line: 4390
Fatal error:
An atom moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
Error on rank 58, will try to stop all ranks
Halting parallel program mdrun_mpi on CPU 58 out of 144
gcq#25: "This Puke Stinks Like Beer" (LIVE)
[cli_58]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 58
I think my simulation crashed possibly due to the large load imbalance generated by the domain decomposition. My system (lipid vesicle with implicit solvent) is highly inhomogeneous, therefore the domain decomposition algorithm will generate highly inhomogeneous domains with some domains empty and some full of particles. I tried to run the simulation with less CPUs (96 cores) and smaller timestep (1 fs) and there wasn't any problem for over 6 million steps.
However, I would still like to use more cores and large timestep to equilibrate my system. Is there any better way to control the load balance and domain decomposition such that I could equilibrate the system more efficiently? The dry martini paper said for such kind of vesicle simulations domain decomposition scheme should be chosen carefully. Is there a guidance for doing so?
Thanks very much.
Please Log in or Create an account to join the conversation.
Time to create page: 0.089 seconds