Did the amber installation pass the test cases?
On Fri, May 31, 2024, 4:36 PM Abdelrahman, Noureen <noureen.unc.edu> wrote:
> This is the error message in my slurm output file:
>
> /var/spool/slurmd/job40159947/slurm_script: line 73: 845284 Killed
> $DO_PARALLEL "$sander" -O -p final_parm.parm7 -c
> carved_frame_100ns.rst7 -o "$output" -r "$restrt" < dummy
> Error: Failed to execute /proj/pierilab/software/amber/amber22/bin/sander
> slurmstepd: error: Detected 2 oom_kill events in StepId=40159947.batch.
> Some of the step tasks have been OOM Killed.
> ~
>
>
>
> Noureen
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Friday, May 31, 2024 4:23 PM
> *To:* Abdelrahman, Noureen <noureen.unc.edu>; AMBER Mailing List <
> amber.ambermd.org>
> *Subject:* Re: [AMBER] Using TCPB with Terachem in Amber
>
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>
> On Fri, May 31, 2024, 3:34 PM Abdelrahman, Noureen via AMBER <
> amber.ambermd.org> wrote:
>
> Dear all,
>
> I am trying to run TCPB with Terachem in Amber. I extracted one frame from
> the Amber MD simulation to use as test. I carried out my MD simulation in
> explicit solvent using the OPC water model. When I run my TCPB calculation,
> the calculation stops abruptly and I get the following message:
> 3. ATOMIC COORDINATES AND VELOCITIES
>
> --------------------------------------------------------------------------------
> Cpptraj Generated Restart
> begin time read from input coords = 0.000 ps
> Number of triangulated 3-point waters found: 5000
>
> --------------------------------------------------------------------------------
> Attached below is my input file:
> Protein QM/MM HF/STO-3G/ff19SB NVE 20 steps (dt=0.5fs, no shake)
> &cntrl
> imin = 0, !no minimization
> irest = 0, !restart
> ntx = 1, !coordinates and velocities are read in
> cut = 9999.9 !non-bonded interactions cutoff
> dt = 0.0005, !0.5fs time step
> ntb = 0, !no periodicity and PME off!
> ntt = 0, !turn off thermostat
> ntpr = 1, !print details to log every step
> ntwx = 1, !write coordinates to mdcrd every 500 steps (every 250fs)
> ntwr = 2, !write restart file at last step
> nstlim = 20, !run for 20 steps
> nscm = 0, !No removal of COM motion,
> ioutfm = 1, !NetCDF MDCRD.
> ntxo = 1, !Formatted ASCII restart file
> ifqnt = 1,
> /
> &qmmm
> qmmask =
> '.2411-2489,1387-1390,908-913,1397-1411,1911-1918,1095-1106,1476-1485,1457-1466,1847-1856',
> qm_theory = 'TERACHEM',
> /
> &tc
> host = 'localhost',
> port = 12345,
> method = 'rhf',
> basis = 'sto-3g',
> debug = 2,
> /
> EOF
>
> Has anyone encountered this before?
> Thanks,
> Noureen
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Received on Fri May 31 2024 - 14:00:02 PDT
