[AMBER] Regarding targeted md

From: Pranabesh Mandal (PhD, Bioinformatics August-2019) <pranabesh.cusb.ac.in>
Date: Tue, 25 Jan 2022 10:00:36 +0530

Dear members,
I am trying to perform a targeted molecular dynamics simulation but my
initial structure is not converging with the final structure.
*.mdin file:*
&cntrl

    imin=0,
    irest=1,
    ntx=5,


    ! Temperature control

    ntt=3,
    gamma_ln=1.0,
    tempi=300.00,

    temp0=300.00,


    ! Potential energy control

    cut=8.0,
    ntb=2,

    ! MD settings

    nstlim=25000,
    dt=0.002,


    ! SHAKE

    ntc=2,
    ntf=2,


    ! Control how often information is printed

    ntpr=100,
    ntwx=100,
    ntwr=10,
    ntxo=2,
    ioutfm=1,


    ! Wrap coordinates when printing them to the same unit cell

    iwrap=1,



    ! Constant pressure control.

    barostat=1,
    ntp=3,
    pres0=1.0,
    taup=1.0,



    ! Constant surface tension (needed for semi-isotropic scaling).
Uncomment
    ! for this feature. csurften must be nonzero if ntp=3 above

    csurften=3,
    gamma_ten=0.0,
    ninterface=2,


    ! Set water atom/residue names for SETTLE recognition

    watnam='WAT',
    owtnm='O',


    itgtmd=1,

    ntr=0,

    tgtrmsd=0.000,

    tgtmdfrc=0.005,

    tgtfitmask=':1-1200',

    tgtrmsmask=':1-1200',

 /



I appreciate all help and look forward to any responses from you.


Thank you
Pranabesh Mandal
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Received on Mon Jan 24 2022 - 21:00:02 PST
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