Dear Anselm,
1. I set up the top files with hydrogen mass repartitioning. Do you think 4
fs needs to be changed (kindly suggest)?
2. While visualization, I used autoimage in cpptraj.
Regards,
Soma
On Fri, Jul 28, 2023 at 11:58 AM Dr. Anselm Horn via AMBER <
amber.ambermd.org> wrote:
> Soma,
>
> two quick comments (as questions):
> 1, Did you setup your top files with hydrogen mass repartitioning, since
> you use a time step of 4 fs? (Otherwise you'll run into problems, of
> course)
> 2, Maybe it is just an visualization issue?
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> Am 28.07.2023 um 09:34 schrieb SOMA ROY via AMBER:
> > Hello Prithviraj,
> >
> > Basically, I aim to understand the interaction of a zinc finger protein
> > with DNA. I have prepared the initial files using CHARMM-GUI.
> >
> > Please find the input file for the production run.
> >
> > A NPT simulation for common production-level simulations
> > &cntrl
> > imin=0, ! No minimization
> > irest=1, ! This IS a restart of an old MD simulation
> > ntx=5, ! So our inpcrd file has velocities
> >
> > ! Temperature control
> > ntt=3, ! Langevin dynamics
> > gamma_ln=1.0, ! Friction coefficient (ps^-1)
> > temp0=303.15, ! Target temperature
> >
> > ! Potential energy control
> > cut=9.0, ! nonbonded cutoff, in Angstroms
> >
> > ! MD settings
> > nstlim=47500000, ! 250 ns total
> > dt=0.004, ! time step (ps)
> >
> > ! SHAKE
> > ntc=2, ! Constrain bonds containing hydrogen
> > ntf=2, ! Do not calculate forces of bonds containing hydrogen
> >
> > ! Control how often information is printed
> > ntpr=1000, ! Print energies every 1000 steps
> > ntwx=25000, ! Print coordinates every 25000 steps to the
> trajectory
> > ntwr=10000, ! Print a restart file every 10K steps (can be less
> > frequent)
> > ! ntwv=-1, ! Uncomment to also print velocities to trajectory
> > ! ntwf=-1, ! Uncomment to also print forces to trajectory
> > ntxo=2, ! Write NetCDF format
> > ioutfm=1, ! Write NetCDF format (always do this!)
> >
> > ! Wrap coordinates when printing them to the same unit cell
> > iwrap=1,
> >
> > ! Constant pressure control.
> > barostat=2, ! MC barostat... change to 1 for Berendsen
> > ntp=1, ! 1=isotropic, 2=anisotropic, 3=semi-isotropic w/
> surften
> > pres0=1.0, ! Target external pressure, in bar
> >
> > ! Set water atom/residue names for SETTLE recognition
> > watnam='WAT', ! Water residues are named WAT
> > owtnm='O', ! Water oxygens are named O
> > /
> >
> > Kindly let me know if I need to provide any other info.
> >
> > Regards,
> > Soma
> >
> > On Thu, Jul 27, 2023 at 6:46 PM Prithviraj Nandigrami <
> > prithviraj.nandigrami.gmail.com> wrote:
> >
> >> Hi,
> >>
> >> Could you tell a bit more about how you set up your system? Also, how
> are
> >> you visualizing the frames?
> >>
> >> On Thu, Jul 27, 2023 at 5:46 AM SOMA ROY via AMBER <amber.ambermd.org>
> >> wrote:
> >>
> >>> Dear AMBER community,
> >>>
> >>> I am trying to simulate a zinc-finger protein. I find in some frames
> that
> >>> zinc ions are moving apart from the protein which should not be the
> case
> >>> here.
> >>>
> >>> Would you please guide me about the procedures needs to be taken in
> this
> >>> case (maybe constraints)?
> >>>
> >>> Regards,
> >>> Soma Roy, Ph.D.
> >>> Max Planck Institute of Molecular Physiology
> >>> Dortmund, Germany
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
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>
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Received on Fri Jul 28 2023 - 06:00:03 PDT
