Hi,
In addition to trying Anselm's advice, are you running this via a
queue (e.g. SLURM or PBS etc)? If so, you may need to increase the
requested walltime for your job. You could also try to speed up the
job by using cpptraj.MPI and 2-4 processes (benchmark on a smaller set
of frames to get an idea of the speedup you can achieve). In general,
I've found that using a number of MPI processes per node equal to the
number of CPU sockets seems to work well.
-Dan
On Mon, Jul 6, 2020 at 12:23 PM Shreeramesh <shreeramesh.gmail.com> wrote:
>
> Dear AMBER Users,
>
> I want to strip water and ions from md.mdcrd file (10000 frames) in cpptraj
> and I used the following script. My job is killed after the 10-40% of
> completion. I request you to kindly help me to fix this error.
>
>
> trajin md.mdcrd
> autoimage
> strip :WAT,Cl-,Na+ outprefix stripped
> trajout md_dry.mdcrd
>
>
> Error:
>
> PARAMETER FILES:
> 0: 'com_solvated.top', 15805 atoms, 4008 res, box: Orthogonal, 3725 mol,
> 3721 solvent, 10000 frames
>
> INPUT TRAJECTORIES:
> 0: 'md.mdcrd' is an AMBER trajectory, Parm com_solvated.top (Orthogonal
> box) (reading 10000 of 10000)
> Coordinate processing will occur on 10000 frames.
>
> OUTPUT TRAJECTORIES:
> 'md_dry.mdcrd' is an AMBER trajectory, Parm com_solvated.top: Writing
> 10000 frames (1-Last, 1)
> TIME: Run Initialization took 0.0001 seconds.
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'com_solvated.top' (2 actions):
> 0: [autoimage]
> Anchor molecule is 1
> The following molecules are fixed to anchor: 2
> 3723 molecules are mobile.
> 1: [strip :WAT,Cl-,Na+ outprefix stripped]
> Stripping 11165 atoms.
> Stripped parm: 'com_solvated.top', 4640 atoms, 285 res, box:
> Orthogonal, 2 mol
> Writing topology 0 (com_solvated.top) to
> 'stripped.com_solvated.top' with format Amber Topology
> ----- md.mdcrd (1-10000, 1) -----
> 0% 10% 20% 30% Killed
>
>
>
>
>
> *Thanks & Regards*
> *Ramesh M*
>
> Email: shreeramesh.gmail.com Mob.: +91-9542200332
> _______________________________________________
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Received on Tue Jul 07 2020 - 07:30:03 PDT
