I suppose that the sander was installed via ambertools24, and the pmemd
was installed via amber24.
Maybe you installed ambertools24 correctly and not installed amber24
correctly.
Non-commercial Amber24 also has pmemd project, but you cannot use GPU to
accelerate the molecular dynamics. In other words, you cannot install
pmemd.cuda project.
On 9/10/24 23:55, Wu, Ming Hsiu via AMBER wrote:
> Hello,
> I downloaded the source code from the official website and installed the non-commercial Amber24 and Amber24Tool on our CentOS server. But I cannot find pmemd in $AMBERHOME/bin/, only sander. The following is the at_summary for the test:
>
> 3033 file comparisons passed
> 2 file comparisons failed (2 of which can be ignored)
> 0 tests experienced errors
> Test log file saved as /data/mwu11/amber/amber24///logs/test_at_serial/2024-09-06_11-21-23.log
> No test diffs to save!
>
> I checked the Link<https://computecanada.github.io/molmodsim-amber-md-lesson/13-Running_Simulations/index.html> where it mentioned that pmemd is only available in commercial AMBER package, but this is not mentioned on the official website. Is it true?
>
> Thanks
> Ming Hsiu Wu
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Received on Tue Sep 10 2024 - 18:30:02 PDT
