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 Mon Apr 29 2019 - 13:30:02 PDT
