On 10/01/2012 7:19 AM, Ben Reynwar wrote:
On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham<mark.abra...@anu.edu.au> wrote:
On 12/19/2011 1:51 PM, Ben Reynwar wrote:
I'm having a problem with gromacs not terminating as expected when
using the maxh option.
It is an REMD simulation with 32 replicas.
I'm specifying -maxh 24 and as expected see the following in the stderr
output.
Step 773882: Run time exceeded 23.760 hours, will terminate the run
Step 773876: Run time exceeded 23.760 hours, will terminate the run
Step 773880: Run time exceeded 23.760 hours, will terminate the run
etc
However I can see that the output files continued to be written for
another hour until at 25 hours the simulation was terminated by the
queueing system.
No checkpoint files were produced. The output files show that the
simulation continued until about step 797000.
I've done similar things previously without running into this problem.
Anyone have any ideas for what stupid mistake I could be making?
Perhaps none. What GROMACS version is this? Does the latest version have the
same behaviour?
Mark
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Sorry for the slow response. I've been away on holiday.
The version used is 4.5.5 with a bug fix applied from
http://lists.gromacs.org/pipermail/gmx-developers/2011-October/005405.html
It was a replica exchange simulation.
I've narrowed down the problem to be specific to using infinite
cutoff. With a finite cutoff there are no problems.
The initial run works fine and creates checkpoints. However a run
started from one of these checkpoints fails to create checkpoints
itself.
All that sounds very much like a bug. Please open an issue here
http://redmine.gromacs.org <http://redmine.gromacs.org/> and attach the
lowest four .tpr and .cpt input files for the failing case. This will
allow someone to find out why and perhaps fix it.
Mark
The diff between the an mdp that works fine and one that doesn't is:
53,57c53,58
< ; [nm] cut-off distance for the short-range neighbor list.
< ; Set to zero for infinite cut-off.
< rlist = 0
< ; Recalculating pair-list is not necessary with an infinite cut-off
< nstlist = 0
---
; [nm] cut-off distance for the short-range neighbor list
; For Generalized Born this must be equal to the cut-off length for
; the born radius calculation.
rlist = 1.6
; [steps] freq to update neighbor list
nstlist = 1
67,68c68,69
< ; infinite coloumb cut-off radius
< rcoulomb = 0
---
; coloumb cutoff radius
rcoulomb = 1.6
76,77c77,78
< ; Infinite VsW cutoff radius.
< rvdw = 0
---
; Increasing VdW cutoff to same as everything else.
rvdw = 1.6
144c145
< rgbradii = 0
---
rgbradii = 1.6
The complete offending mdp file will follow.
Also if there's anything stupid in here unrelated to my current
problem, please let me know too :).
; 7.3.2 Preprocssing
; ------------------
; Apply constaint to alpha carbon atoms in alpha-crystalline domain.
define = -DALPHACRYST_POSRES -DCHIRRES
; 7.3.3 Run Control
; -----------------
; group(s) for center of mass motion removal
comm_grps = System
; Do Langevin dynamics.
integrator = sd
; maximum number of steps to integrate
nsteps = 100000000
; remove center of mass translation and rotation around centre of mass
comm_mode = Angular
; [ps] time step for integration
dt = 0.002
; [steps] frequency of mass motion removal
nstcomm = 10
; [ps] starting time for run
tinit = 0
; 7.3.4 Langevin Dynamics
; -----------------------
; Use PID to seed random number.
ld_seed = -1
; 7.3.8 Output Control
; --------------------
; [steps] freq to write velocities to trajectory
nstvout = 0
; [steps] freq to write energies to log file
nstlog = 1000
; [steps] freq to write energies to energy file
nstenergy = 1000
; group(s) to write to xtc trajectory
xtc_grps = System
; [real] precision to write xtc trajectory
xtc_precision = 1000
; [steps] freq to write coordinates to xtc trajectory
nstxtcout = 1000
; [steps] freq to write coordinates to trajectory
nstxout = 0
; group(s) to write to energy file
energygrps = System
; [steps] freq to write forces to trajectory
nstfout = 0
; 7.3.9 Neighbour Searching
; -------------------------
; [nm] cut-off distance for the short-range neighbor list.
; Set to zero for infinite cut-off.
rlist = 0
; Recalculating pair-list is not necessary with an infinite cut-off
nstlist = 0
; method of updating neighbor list
ns_type = grid
; no periodic boundary conditions
pbc = no
; 7.3.10 Electrostatics
; ---------------------
; apply a cut-off to electostatic
coulombtype = cut-off
; infinite coloumb cut-off radius
rcoulomb = 0
; 7.3.11 VdW
; ----------
; Dispersion correction makes no sense without box size.
DispCorr = no
; twin-range cut-off with rlist where rvdw>rlist
vdwtype = cut-off
; Infinite VsW cutoff radius.
rvdw = 0
; 7.3.13 Ewald
; ------------
; [nm] grid spacing for FFT grid when using PME
fourierspacing = 0.12
; relative strength of Ewald-shifted potential at rcoulomb
ewald_rtol = 1e-05
; interpolation order for PME, 4 cubic
pme_order = 4
; 7.3.14 Temperature Coupling
; ---------------------------
; Temperature.
ref_t = 600.0
; temperature coupling frequency
nsttcouple = 1
; Thermostat is already taken care of by langevin dynamics.
tcoupl = no
; couple everything to same bath
tc_grps = System
; [ps] time constant for coupling
tau_t = 1
; 7.3.15 Pressure Coupling
; ------------------------
; [bar] reference pressure for coupling
ref_p = 1.0
; pressure coupling in x-y-z directions
pcoupltype = isotropic
; [ps] time constant for coupling
tau_p = 2.0
; no pressure coupling if using generalized born
pcoupl = no
; [bar^-1] compressibility
compressibility = 4.5e-05
; 7.3.17 Velocity Generation
; --------------------------
; velocity generation turned off
gen_vel = no
; 7.3.18 Bonds
; ------------
; apply constraints to the start configuration
continuation = yes
; All bonds are constraints
constraints = allbonds
; [degrees] maximum angle that a bond can rotate before LINCS will complain
lincs_warnangle = 30
; highest order in the expansion of the contraint coupling matrix
lincs_order = 4
; number of iterations to correct for rotational lengthening
lincs_iter = 1
; LINear Constraint Solver
constraint_algorithm = LINCS
; 7.3.22 NMR refinement (dihedral restraints not in manual)
; ---------------------------------------------------------
; scaling factor for force constant for dihedral constraints
dihre-fc = 10
; Set chirality and omega angle restraints.
dihre = yes
; 7.3.27 Implicit Solvent
; -----------------------
; The cutoff radius for calculating the Born radii (must be equal to rlist).
rgbradii = 0
; Use a Generalized Born Solvent
implicit_solvent = GBSA
; Use the Onufriev-Bashford-Case method to calculate the Born radii
gb_algorithm = OBC
; Dielectric constant for implicit solvent.
; Default is 80 but we use 78.5 for consistency with amber.
gb_epsilon_solvent = 78.5
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