Hi,
Those kinds of errors are usually the result of running out of memory,
although it's not clear to me why that might be happening here. Can
you provide me off-list a topology and a few trajectory frames so I
can try to reproduce the error? Thanks.
-Dan
On Mon, Apr 29, 2019 at 4:26 PM Debarati DasGupta
<debarati_dasgupta.hotmail.com> wrote:
>
> I am using spam to calculate free energies for a mixed solvent MD simulation
> My input file is as follows:
> parm 3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_9pmemdcuda/3kfa_layer_ACN_H2O_5-95vv.prmtop
> trajin 3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4G_production.1.crd 1 50 1
> trajin 3_mixMD/ablkinase_3KFA/ACN_H2O_5-95vv_layered/3kfa_md_1-pmemdMPI/New4H_production.1.crd 1 50 1
> autoimage
>
> ##Align trajectory to reference structure by minimizing RMSD
> reference 3kfa_layer_ACN_H2O_5-95vv.pdb
> strip :Cl-,Na+
> rms reference mass out 3kfa_ACN_15-20ns_md_CA_rmsd.txt :1-286.CA
> volmap volmap_C3N.xplor 0.5 0.5 0.5 :C3N.C2 name GRID size 200,200,200 peakcut 0.0001 peakfile ACN_peak.xyz
> spam ACN_peak.xyz solv C3N reorder cut 12 sphere site_size 6 dgbulk -30.3 dhbulk -22.2 info info.txt summary spam_summary.out out spam_energies.out
>
> Error I get is:
>
> Read 1000 frames and processed 1000 frames.
> TIME: Avg. throughput= 16.8114 frames / second.
>
> ACTION OUTPUT:
> SPAM timing data:
> TIME: Residue c.o.m. calc: 0.0058 s ( 0.02%)
> TIME: Peak assignment : 0.0196 s ( 0.07%)
> TIME: Occupancy calc. : 0.0013 s ( 0.00%)
> TIME: Energy calc : 27.4013 s ( 99.89%)
> TIME: Residue reordering : 0.0040 s ( 0.01%)
> TIME: SPAM Action Total: 27.4324 s
> terminate called after throwing an instance of 'std::bad_alloc'
> what(): std::bad_alloc
> Aborted (core dumped)
>
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Received on Tue Apr 30 2019 - 06:30:02 PDT
