[gmx-users] maxh not causing termination

Mon Jan 9 23:46:43 CET 2012

On 10/01/2012 7:19 AM, Ben Reynwar wrote:
> On Tue, Dec 20, 2011 at 7:16 PM, Mark Abraham<Mark.Abraham at 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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