This could perhaps be a wrapping issue.
Try to process the trajectory first by “autoimage” followed by rms fitting
in cpptraj.
On Thursday, 4 September 2025, YASHIKA . via AMBER <amber.ambermd.org>
wrote:
> Respected Team,
>
> I am facing an issue while analyzing my trajectories. After running
> equilibration under NVT (pmemd.cuda), I used cpptraj to convert the final
> .rst7 file to .pdb. The structure looks abnormal (screenshot attached).
> However, when I performed the production run under NPT (pmemd.cuda) and
> analyzed the .rst7 file with cpptraj in the same way, the output structure
> looks normal (screenshot attached).
>
> I am not sure why there is such a difference in visualization between the
> equilibration and production structures. Could this be related to imaging,
> wrapping, or my input parameters?
>
> Below are my input files:
>
> Equilibrate the system for 10ns
> &cntrl
> nstlim=5000000, dt=0.002, ntx=5, irest=1, ntpr=1500, ntwr=1500,
> ntwx=50000, ntxo=2, ioutfm=1,
> tempi=300.0, temp0=300.0, ntt=3, gamma_ln=1.0,
> ntb=1, ntp=0, ig=-1,
> cut=18,
> ntc=2, ntf=2,
> nrespa=1,
> ntr=0
> /
>
> Constant pressure constant temperature production run for 10ns
> &cntrl
> nstlim=5000000, dt=0.002, ntx=5, irest=1, ntpr=1000, ntwr=1000,
> ntwx=25000, gamma_ln=1.0,
> temp0=300.0, ntt=3, tautp=2.0,
> ntb=2, ntp=1,
> cut=18,
> ntc=2, ntf=2,
> nrespa=1,
> &end
>
> Both equilibration and production were run using *pmemd.cuda.*
>
> Could anyone please explain why the structures appear so different between
> equilibration and production? Is this expected behavior due to
> imaging/periodic boundary conditions, or am I missing something? If anyone
> has encountered this before, I would really appreciate your advice.
>
> Thank you in advance for your help.
>
> With regards,
>
> Yashika
>
--
Best Regards
Elvis
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Received on Wed Sep 03 2025 - 23:00:04 PDT
