Could you try a “cubic” simulation box instead of an “octahedral”??
The former is more suitable for elongated proteins, while the latter is suitable for globular proteins.
Rest of the parameters and settings could be same.
Hope this helps.
Best Regards
Elvis
> On 6 May 2026, at 12:08, Surabhi Singh 24933024 via AMBER <amber.ambermd.org> wrote:
>
> Hello Amber Team,
>
> I am working on a protein–DNA complex (bHLH transcription factor). During
> the production run, I observe that the longer helical region becomes highly
> flexible and shows noticeable bending near the center.
>
> Protocol followed:
>
> 1. Forcefield used : Amber: ff19SB, OL24, TIP3P water model
> 2. Salt conc: 150mM Nacl
> 3. Energy minimization
> 4. Three equilibration stages (~1.15 ns total, first two with restrain
> and last one without restrain)
> 5. Production MD: 250 ns (trajectory appears stable overall)
>
>
> The total and potential energies remain stable with no significant
> deviations, yet the helix undergoes bending.
>
> Question:
> 1. How should this bending be interpreted despite stable energy profiles?
> Is this expected behavior (e.g., intrinsic flexibility), or could it
> indicate an issue with the setup?
>
> Thank you for your guidance.
>
> Thanks and Regards
> Surabhi Singh
> Ph.D. Computational Biology
> Biosciences and Bioengineering, IIT Roorkee
> <wild.png>
> <bend.png>
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Received on Wed May 06 2026 - 00:00:04 PDT
