What happens when you run this? What is the final rmad,and restraint
energy? The force constant is quite small.
On Mon, Jan 24, 2022, 11:30 PM Pranabesh Mandal (PhD, Bioinformatics
August-2019) <pranabesh.cusb.ac.in> wrote:
> 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 Tue Jan 25 2022 - 04:30:02 PST
