How long time does quasi harmonic calculations take?

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mk_KIM

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Jul 10, 2024, 3:36:59 AM7/10/24
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I ran Generalized Born (GB) with quasi-harmonic calculations for a 20 amino acid (AA) peptide and a 400 AA long antibody complex using 101 frames.

However, my terminal has been in this state for about 2 hours with my CPU running continuously. 

Is this normal, or could there be some kind of error occurring? I have copied my command lines below with pictures. Any help would be greatly appreciated.




[INFO   ] Selecting residues by distance (10 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 102 residues:
R:A:GLY:1   R:A:GLU:2   R:A:GLU:3   R:A:SER:4   R:A:ALA:5   R:A:SER:6   R:A:SER:7   R:A:GLY:8   R:A:LYS:9   R:A:LEU:10
R:A:GLY:11  R:A:LEU:12  R:A:ILE:13  R:A:THR:14  R:A:ASN:15  R:A:THR:16  R:A:ILE:17  R:A:ALA:18  R:A:GLY:19  R:A:VAL:20
R:A:ALA:21  R:A:GLY:22  R:A:LEU:23  R:A:ILE:24  R:A:THR:25  L:B:GLN:1   L:B:LEU:2   L:B:VAL:3   L:B:LEU:24  L:B:SER:25
L:B:ARG:26  L:B:GLN:27  L:B:HIS:28  L:B:SER:29  L:B:THR:30  L:B:TYR:31  L:B:THR:32  L:B:ILE:33  L:B:GLU:34  L:B:TYR:36
L:B:TYR:46  L:B:MET:48  L:B:GLU:49  L:B:LEU:50  L:B:LYS:51  L:B:LYS:52  L:B:ASP:53  L:B:GLY:54  L:B:SER:55  L:B:HIS:56
L:B:SER:57  L:B:SER:70  L:B:GLY:72  L:B:ARG:75  L:B:GLY:93  L:B:VAL:94  L:B:GLY:95  L:B:ASP:96  L:B:THR:97  L:B:ILE:98
L:B:LYS:99  L:B:GLU:100 L:B:GLN:101 L:B:PHE:102 L:B:VAL:103 L:B:TYR:104 L:B:ALA:159 L:B:PHE:160 L:B:SER:161 L:B:SER:162
L:B:TYR:163 L:B:ASP:164 L:B:MET:165 L:B:SER:166 L:B:TRP:178 L:B:ALA:180 L:B:TYR:181 L:B:ILE:182 L:B:SER:183 L:B:ARG:184
L:B:GLY:185 L:B:GLY:186 L:B:GLY:187 L:B:TYR:188 L:B:THR:189 L:B:TYR:190 L:B:ARG:203 L:B:ASN:205 L:B:SER:228 L:B:ARG:229
L:B:HIS:230 L:B:ILE:231 L:B:TYR:232 L:B:TYR:233 L:B:GLY:234 L:B:SER:235 L:B:SER:236 L:B:HIS:237 L:B:TYR:238 L:B:TYR:239
L:B:ALA:240 L:B:MET:241

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 101 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 9 CPUs...

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /Users/mkkim/mambaforge/envs/gmx_MMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########| 101/101 [elapsed: 01:20 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########| 101/101 [elapsed: 00:03 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########| 101/101 [elapsed: 01:36 remaining: 00:00]
[INFO   ] Beginning quasi-harmonic calculations with /Users/mkkim/mambaforge/envs/gmx_MMPBSA/bin/cpptraj    D2BEBE54-CD45-49D7-B62B-DA0BB78163A7.jpeg

marioe911116

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Jul 10, 2024, 2:11:45 PM7/10/24
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yep, quasiharmonic calculations takes a long time
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