In addition to what everyone has said/suggested, there is a script
that attempts to automate a preparation protocol for explicitly
solvated systems with the goal of getting them ready for production
dynamics: https://github.com/drroe/AmberMdPrep
If you're having issues relaxing your system, give the script a try.
-Dan
On Thu, Sep 4, 2025 at 6:35 AM Carlos Simmerling via AMBER
<amber.ambermd.org> wrote:
>
> Please see the ambermd.org web site for a detailed tutorial on how to
> properly equlibrate the solvated system. You have not mentioned the details
> of your protocol to relax the system density, but this is a necessary step
> even for NVT production runs.
>
> On Thu, Sep 4, 2025, 1:32 AM 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
> > _______________________________________________
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Received on Thu Sep 04 2025 - 09:00:02 PDT
