Thank you very much Anselm,
Only for more clearer understanding. The dimer protein showed a monomer
transition and may stay in this state. Experimentally, it is a normal
behavior. What about the RMSD and RMSF analyses. A part of one monomer
appears to be dangling over the periodic box. Does this situation need to
autoimage the two monomers in cpptraj.
Thank you again.
Ibrahim
On Thu, Jan 9, 2025 at 7:58 PM Dr. Anselm Horn via AMBER <amber.ambermd.org>
wrote:
> Ibrahim,
>
> the behaviour of your dimer is quite common in MD simulations:
> If a molecular entity moves outside the periodic box, it gets imaged
> into the box again at the opposite site, i.e. wrapped; this happens not
> only for solvent molecules, but also in oligomeric species. The energy,
> however, is unaffected, since the interaction of the molecules in the
> simulation box with the molecules in the surrounding boxes is taken into
> account.
>
> For postprocessing, you want an intact dimer complex, of course. This
> can be achieved by imaging (e.g. autoimage in cpptraj).
> Alternatively you can unwrap the trajectory via cpptraj. Please consult
> the Amber manual for a detailed description.
> (Remove the solvent molecules *prior* to such a step in order to
> minimize the system's size and save computational time.)
>
> Hope that helps.
>
> Good luck,
>
> Anselm
>
> Bioinformatik
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 09.01.2025 um 18:30 schrieb Ibrahim Said via AMBER:
> > Dear Amber users
> > I am running a homodimer protein for 100 ns. Upon 65 ns simulation, the
> > dimer has dissociated to two monomers (no problem). The 1st monomer has
> > nearly moved out the water simulation box. In the next 15 ns this monomer
> > alternates between outside and inside the simulation box to form the
> dimer
> > again. Does this movement outside the box affect the subsequent
> > calculations? And if so can I re-image the dimer and re-run the
> simulation
> > process at the time of separation?. I am using the ff14SB forcefield and
> > the medium of simulation is physiological saline. The Amber version is
> > AMBER16.
> > Please, any help is thankful
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>
>
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Received on Thu Jan 09 2025 - 12:30:02 PST
