Add 12-6-4 support for the Energy/Emin/Ene_Decomp commands in cpptraj

[pengfeili1]

Hi Dan,

Finally I found a time to add the 12-6-4 support to the Energy/Emin/Ene_Decomp commands in cpptraj on GitHub. Can you approve this pull request? Thanks!

Best,
Pengfei

[drroe]

This looks great Pengfei!

If it's not too much trouble, can you please add a test case that calculates 12-6-4 energies? I went a slightly different route in my new branch for adding LJ C parameters, and when I'm merging your code in I want to make sure I don't break anything.

If you'd rather I just merge this in I can do that and we can add the test cases after.

[drroe]

I'll just go ahead and merge this for now and work on adding some tests. I also need to increment the version number.

Thanks again!

[drroe]

@pengfeili1 I wasn't able to reproduce the VDW energies I get in sander with the VDW energies that CPPTRAJ produces when LJ C coefficients are present (although the 1-4 terms look OK). Can you please take a look? I'm attaching a tarball that contains the topology and restart I am testing with, along with a script to run everything. Let me know if you need anything else.
CannotReproduceLj1264.tar.gz

[drroe]

One note - to better reproduce the total electrostatic energy between sander/cpptraj decrease the direct sum tolerance in both to 0.00001

[drroe]

FYI I started adding LJ 12-6-4 to my version 7 branch (https://github.com/drroe/cpptraj/tree/prepareforleap.remote.buildatom) using your previous commit #1159 as notes and I'm testing against sander as I go. I will hopefully have it done tomorrow.

[pengfeili1]

Hi Dan, Thank you for the follow up. I did a test for the nobox one, it is because you used igb=6, which may actually silence the lj1264=1 setting. If you doing the calculation in gas phase (deleting the whole line about igb in the sander input), you will get the same results with cpptraj. For the box one, it seems sander considers the C4 terms into account, but cpptraj does not. I found that by testing lj1264=0 for the sander input file. Hope these information is helpful for the debugging. Best, Pengfei

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On Feb 5, 2026, at 1:56 PM, Daniel R. Roe ***@***.***> wrote: drroe left a comment (Amber-MD/cpptraj#1159) <#1159 (comment)> FYI I started adding LJ 12-6-4 to my version 7 branch (https://github.com/drroe/cpptraj/tree/prepareforleap.remote.buildatom) using your previous commit #1159 <#1159> as notes and I'm testing against sander as I go. I will hopefully have it done tomorrow. — Reply to this email directly, view it on GitHub <#1159 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABUMM2PF45S3LV4YUABCWDL4KON6FAVCNFSM6AAAAACUASYB46VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQNJVHA4DSOJVGM>. You are receiving this because you were mentioned.