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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Received on Fri Jul 28 2023 - 03:00:02 PDT
