[gmx-users] minimization and simulation problems
Chris Neale
chris.neale at utoronto.ca
Mon Apr 4 18:20:19 CEST 2011
Can you please redo the md part with gen_vel=yes and see if that makes
any difference?
Generally, you need to narrow down the problem for us. Does it crash in
serial as well as parallel? How many steps does it go before the crash?
what happens to the system volume as a function of time for the duration
of the simulation prior to the crash.
Chris.
Quoting politr at fh.huji.ac.il
<http://lists.gromacs.org/mailman/listinfo/gmx-users>:
Dear gromacs users,
>/ my box dimensions are 368A and when I run the simulation with
/>/ nsteps=1 it works fine. The mdp files used for minimization and
/>/ post-em simulation are attached.
/Thanks again for your help.
Regina
>/
/>/
/>/ Quotingchris.neale at utoronto.ca <http://lists.gromacs.org/mailman/listinfo/gmx-users>:
/>/
/>>/ What are your initial box dimensions prior to em? Also, please copy
/>>/ and paste your .mdp options. Also, what happens when you run the
/>>/ same post-em simulation with nsteps=1 ?
/>>/
/>>/ -- original message --
/>>/
/>>/
/>>/ Dear all,
/>>/ I'm trying to run simulation of 30 proteins in water using the Martini
/>>/ force field. I used water.gro file in order to solvate the proteins.
/>>/ For minimization I used the em.mdp file published at Martini site
/>>/ (http://md.chem.rug.nl/cgmartini/index.php/home). When I set the emtol
/>>/ parameter to 10 the system can't converge. So I used emtol 100 and
/>>/ then the system converged. I use it as an input for the simulation.
/>>/ The file can't be attached as it is too big nut I can send it if needed.
/>>/ However, the sumulation crushes when I'm trying to run MD using md.mdp
/>>/ also from the Martini site. I'm getting the following warnings and
/>>/ errors:
/>>/ Warning: Only triclinic boxes with the first vector parallel to the
/>>/ x-axis and the second vector in the xy-plane are supported.
/>>/ Box (3x3):
/>>/ Box[ 0]={ nan, nan, nan}
/>>/ Box[ 1]={ nan, nan, nan}
/>>/ Box[ 2]={ nan, nan, nan}
/>>/ Can not fix pbc.
/>>/ Warning: Only triclinic boxes with the first vector parallel to the
/>>/ x-axis and the second vector in the xy-plane are supported.
/>>/ Box (3x3):
/>>/ Box[ 0]={ nan, nan, nan}
/>>/ Box[ 1]={ nan, nan, nan}
/>>/ Box[ 2]={ nan, nan, nan}
/>>/ Can not fix pbc.
/>>/ Warning: Only triclinic boxes with the first vector parallel to the
/>>/ x-axis and the second vector in the xy-plane are supported.
/>>/ Box (3x3):
/>>/ Box[ 0]={ nan, nan, nan}
/>>/ Box[ 1]={ nan, nan, nan}
/>>/ Box[ 2]={ nan, nan, nan}
/>>/ Can not fix pbc.
/>>/ Warning: Only triclinic boxes with the first vector parallel to the
/>>/ x-axis and the second vector in the xy-plane are supported.
/>>/ Box (3x3):
/>>/ Box[ 0]={ nan, nan, nan}
/>>/ Box[ 1]={ nan, nan, nan}
/>>/ Box[ 2]={ nan, nan, nan}
/>>/ Can not fix pbc.
/>>/ Warning: Only triclinic boxes with the first vector parallel to the
/>>/ x-axis and the second vector in the xy-plane are supported.
/>>/ Box (3x3):
/>>/ Box[ 0]={ nan, nan, nan}
/>>/ Box[ 1]={ nan, nan, nan}
/>>/ Box[ 2]={ nan, nan, nan}
/>>/ Can not fix pbc.
/>>/ Warning: Only triclinic boxes with the first vector parallel to the
/>>/ x-axis and the second vector in the xy-plane are supported.
/>>/ Box (3x3):
/>>/ Box[ 0]={ nan, nan, nan}
/>>/ Box[ 1]={ nan, nan, nan}
/>>/ Box[ 2]={ nan, nan, nan}
/>>/ Can not fix pbc.
/>>/
/>>/ -------------------------------------------------------
/>>/ Program mdrun_mpi, VERSION 4.0.3
/>>/ Source code file: nsgrid.c, line: 348
/>>/
/>>/ Fatal error:
/>>/ Number of grid cells is zero. Probably the system and box collapsed.
/>>/
/>>/ -------------------------------------------------------
/>>/
/>>/ "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ Error on node 0, will try to stop all the nodes
/>>/ Halting parallel program mdrun_mpi on CPU 0 out of 8
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0[cli_0]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
/>>/
/>>/ -------------------------------------------------------
/>>/ Program mdrun_mpi, VERSION 4.0.3
/>>/ Source code file: nsgrid.c, line: 348
/>>/
/>>/ Fatal error:
/>>/ Number of grid cells is zero. Probably the system and box collapsed.
/>>/
/>>/ -------------------------------------------------------
/>>/ Error on node 1, will try to stop all the nodes
/>>/ Halting parallel program mdrun_mpi on CPU 1 out of 8
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3[cli_3]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 3
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5[cli_5]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 5
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4[cli_4]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 4
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6[cli_6]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 6
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2[cli_2]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 2
/>>/
/>>/ gcq#166: "It Wouldn't Hurt to Wipe Once In a While" (Beavis and Butthead)
/>>/
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1[cli_1]:
/>>/ aborting job:
/>>/ application called MPI_Abort(MPI_COMM_WORLD, -1) - process 1
/>>/
/>>/ When I looked at the pdb file attached I see something strange that is
/>>/ happening at the edges of the box.
/>>/ I can't understand what is the problem. Can someone help me with it?
/>>/ Thank you in advance.
/>>/ Regina
/>>/
/>>/ ----------------------------------------------------------------
/>>/ This message was sent using IMP, the Internet Messaging Program.
/>>/
/>>/ ----------------------------------------------------------------
/>>/
/>>/ --
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/>>/ http://lists.gromacs.org/mailman/listinfo/gmx-users
/>>/ Please search the archive at
/>>/ http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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/>/
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-------------- next part --------------
;
; STANDARD MD INPUT OPTIONS FOR MARTINI 2.0
;
; for use with GROMACS 3.3
;
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
; MARTINI - Most simulations are stable with dt=40 fs,
; some (especially rings) require 20-30 fs.
; The range of time steps used for parametrization
; is 20-40 fs, using smaller time steps is therefore not recommended.
integrator = steep
; start time and timestep in ps
tinit = 0.0
dt = 0.025
nsteps = 1000000
; number of steps for center of mass motion removal =
nstcomm = 1
comm-grps =
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 5000
nstvout = 5000
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 1000
nstenergy = 1000
; Output frequency and precision for xtc file =
nstxtcout = 1000
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps =
; NEIGHBORSEARCHING PARAMETERS =
; MARTINI - no need for more frequent updates
; or larger neighborlist cut-off due
; to the use of shifted potential energy functions.
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; MARTINI - vdw and electrostatic interactions are used
; in their shifted forms. Changing to other types of
; electrostatics will affect the general performance of
; the model.
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; MARTINI - normal temperature and pressure coupling schemes
; can be used. It is recommended to couple individual groups
; in your system seperately.
; Temperature coupling =
tcoupl = no
Pcoupl = no
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 320
gen_seed = 473529
; OPTIONS FOR BONDS =
; MARTINI - for ring systems constraints are defined
; which are best handled using Lincs.
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
emtol = 10
-------------- next part --------------
; VARIOUS PREPROCESSING OPTIONS =
title = Martini
cpp = /usr/bin/cpp
; RUN CONTROL PARAMETERS =
integrator = md
; start time and timestep in ps =
tinit = 0.0
dt = 0.030
nsteps = 1000000
; number of steps for center of mass motion removal =
nstcomm = 1
; Groups for center of mass motion removal
comm-grps = System
; OUTPUT CONTROL OPTIONS =
; Output frequency for coords (x), velocities (v) and forces (f) =
nstxout = 100
nstvout = 100
nstfout = 0
; Output frequency for energies to log file and energy file =
nstlog = 100
nstenergy = 100
; Output frequency and precision for xtc file =
nstxtcout = 100
xtc_precision = 100
; This selects the subset of atoms for the xtc file. You can =
; select multiple groups. By default all atoms will be written. =
xtc-grps =
; Selection of energy groups =
energygrps = Protein_PSE W_ION
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist = 10
; ns algorithm (simple or grid) =
ns_type = grid
; Periodic boundary conditions: xyz or none =
pbc = xyz
; nblist cut-off =
rlist = 1.2
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon_r = 15
; Method for doing Van der Waals =
vdw_type = Shift
; cut-off lengths =
rvdw_switch = 0.9
rvdw = 1.2
; Apply long range dispersion corrections for Energy and Pressure =
DispCorr = No
; OPTIONS FOR WEAK COUPLING ALGORITHMS =
; Temperature coupling =
tcoupl = Berendsen
; Groups to couple separately =
tc-grps = Protein_PSE W_ION
; Time constant (ps) and reference temperature (K) =
tau_t = 1.0 1.0
ref_t = 300 300
; Pressure coupling =
Pcoupl = berendsen
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar) =
tau_p = 1.0 1.0
compressibility = 5e-5
ref_p = 1.0 1.0
; GENERATE VELOCITIES FOR STARTUP RUN =
gen_vel = no
gen_temp = 300
gen_seed = 473529
; OPTIONS FOR BONDS =
constraints = none
; Type of constraint algorithm =
constraint_algorithm = Lincs
; Do not constrain the start configuration =
unconstrained_start = no
; Highest order in the expansion of the constraint coupling matrix =
lincs_order = 4
; Lincs will write a warning to the stderr if in one step a bond =
; rotates over more degrees than =
lincs_warnangle = 30
-------------- next part --------------
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