[gmx-users] No Checkpoint File generated

[Mark Abraham]

On Fri, Aug 21, 2015 at 5:56 AM Chunlei ZHANG <chunleizhang.pku at gmail.com>
wrote:

> Dear All,
>
> I am doing a md simulation for a system consisting of protein with 1.5ns
> thick water shell.
> The whole system is simulated in vacuum.
> I turn of PBC and cutoffs for nonbond interactions.
>
> Now, the simulation runs well, but no checkpoint file is output.
> Does anyone know the issue?
> The parameters in .mdp file is appended.
>

Only how you ran the simulation on your infrastructure matters. mdrun
always writes a checkpoint unless you use -noconfout.

Mark


>
> Thanks in advance.
>
> Chunlei
>
>
> *********************************************************************************************
>
> define = -DPOSRES -DFPOSRES ; position restrain the protein
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 250000 ; 2 *  25 000 = 50 ps
> dt = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 0 ; save coordinates every 1 ps
> nstvout = 0 ; save velocities every 1 ps
> nstxtcout = 500 ; save compressed coordinates very 1 ps
> nstenergy = 500 ; save energies every 1 ps
> nstlog = 500 ; update log file every 1 ps
> ; Bond parameters
> continuation = no ; continue from nvt run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
> lincs_iter = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = simple ; search neighboring grid cels
> nstlist = 0 ; 10 fs
> rlist = 0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 0 ; short-range electrostatic cutoff (in nm)
> rvdw = 0 ; short-range van der Waals cutoff (in nm)
> vdwtype = cut-off ; twin-range cut-off for vdw interation
> coulombtype = cut-off ; Particle Mesh Ewald for long-range electrostatics
> ; Temperature coupling is on
> tcoupl = V-rescale ; modified Berendsen thermostat
> tc-grps = Protein SOL RWW ; two coupling groups - more accurate
> tau_t = 0.1 0.1 0.1 ; time constant, in ps
> ref_t = 300 300 300 ; reference temperature, one for each group, in K
> ; Pressure coupling is off
> pcoupl = no ; no pressure coupling in NVT
> ; Periodic boundary conditions
> pbc = no ; 3-D PBC
> comm_mode       = ANGULAR
> nstcomm         = 1
> --
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