GROMACS version: 2020
GROMACS modification: No
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Dear All,
I would like to know how long it takes to complete the gmx do_dssp analysis for a 100 ns and 200 ns protein simulation data?
Is there any way to check the estimated time of completion or etc. if it’s too long ?
I’m using gromacs version 2020 and running dssp-2.0.4-linux-amd64.
any info is much appreciated. Thank you.
Depending on how frequently you saved frames, the analysis can take several hours. do_dssp is just a wrapper that calls dssp for every frame, dumping a temporary PDB file, running the analysis, and collating the result. It’s very inefficient, especially since it requires disk I/O at every step.
How can I determine/ check how much saved frames for the trajectory input file (.xtc) ?
It’s been over 2 days for my dssp analysis and it’s still in progress. I’m running two 100 ns (2.3 GB data) and two 200 ns (4.8 GB data) at once in separate computers, 62.7 GB and 125.7 GB memory with 12 TB and 6 TB available storage respectively. Do you think it’s reasonable/normal?
No, that’s not reasonable. Are you getting temp file output?
Yes. There are 4 temp files output but all 0 bytes data. its been almost 2 weeks and still running.
currently I’m running it on dssp-2.0.4-linux-amd64. Should I try with another same version dssp-2.0.4-linux-i386? or any solution?
There is no reason for do_dssp to take more than a few hours. Several people have reported the same behavior so maybe something is buggy. Try upgrading to 2020.3 and try again.
I have upgraded to gromacs 2020.3 unfortunately it’s still the same. What can I do? Any suggestion?
Have you confirmed that your dssp binary works as a standalone executable?
Yes I believe it is working good. Unfortunately, unlike in gromacs function do_dssp several days waiting still in progress.
What should I do?