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### In which tool?
_No response_
### New Feature
* create *.yaml file with all the gmx_MMPBSA dependencies... this should simplify the installation procedure...
check this [thread](https://stack…
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I used gmx_MMPBSA for calculating the binding free energy between RNA and protein for 2500 frames using 5ns of trajectory as input. PBC was removed and the trajectory was fitted. The command used wa…
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The Hierarchical Data Format File (h5) becomes considerably slow when decomposition data is saved. Specifically, it is extremely inefficient for both writing and reading for the per-wise scheme. It is…
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### My Question is...
Can I get GBSA value for every frame in the trajectory?
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I am seeing that slurm is close to kill a job running for 15 days and I wondered about how to resume the PBSA calculations after. Looking to --help I wondered if maybe -rewrite-output could do it... b…
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I was running this command,
nohup mpirun -np 8 gmx_MMPBSA MPI -O -i mmgbsa_5frames.in -cs sys.pdb -ci
prot_rna_dna.ndx -cg 1 15 -ct
fnrna-dna_0-500ns_norest-350-400_nopbc_compact_fit_dt1ns.xtc -cp…
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### Bug summary
I get nothing written in the output file however the run seems to take all the time it needs.
### Terminal output
```bash
I get this as the last line in my slurm file as I am runni…
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### Bug summary
I am using gmx_MMPBSA 1.5.1
I am trying to run the example Protein_ligand_CHARMMff.
It works when the line #PBRadii=7 is commented but when it is uncommented I have an error about r…
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Dear Sir
I hope this quey finds you well
I have an enzyme-ligabd compkex with a Zn atoms in the pocket. When I tried to calculate MMGBSA I got a postive values. MD simulation inputs were generated…
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### My Question is...
When I was running the gmx_MMPBSA inparallel using the following command it gives the error
mpirun -np 2 gmx_MMPBSA MPI -O -i mmpbsa.in -cs com.tpr -ci index.ndx -cg 19 20 …