I am very confused after autoimage it shows same drops in the rmsd at the
same time point. Please look at the input files also may be i have to
change the parameters.
On Mon, Dec 21, 2020 at 12:39 PM Syeda Amna Arshi <seyydaamnaarshi.gmail.com>
wrote:
> I think that my complex has been moving out of the octahedron water box
> (TIP3PBOX) during the simulation, it looks like part of the complex goes
> out of the box at many points. Are there any parameters in my input files
> that I should try adjusting?
> Here are the settings that I used for my input files
>
> --complex initial minimization solvent + ions
> &cntrl imin = 1,maxcyc = 3000,ncyc = 1500,ntb = 1,ntr = 1,cut
> = 10.0/
> Hold the Protein + DNA fixed
> 100.0
> RES 1 153
> END
> END
>
> --complex initial minimization solvent + ions
> &cntrl imin = 1,maxcyc = 5000,ncyc = 2500,ntb = 1,ntr = 1,cut
> = 10.0/
> Hold the Protein + DNA fixed
> 25.0
> RES 1 153
> END
> END
>
> --Complex minimization for whole system without restraint
> &cntrl imin = 1,maxcyc = 5000,ncyc = 2500,ntb = 1,ntr = 0,cut
> = 10.0/
>
>
> --complex: 20ps MD with res on the protein + DNA complex
> &cntrl
> imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10.0,
> ntr = 1, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0,ntt
> = 3, gamma_ln = 1.0, nstlim = 10000, dt = 0.002, ntpr = 10000, ntwx =
> 10000, ntwr = 10000,
>
> /
> Keep DNA fixed with weak restraints
> 10.0
> RES 1 153
> END
> END
>
>
> --complex: 80ps MD with 0.5 Kcal res on protein + DNA complex
> &cntrl
> imin = 0, irest = 1, ntx = 7, ntb = 1, cut = 10.0,
> ntr = 1, ntc = 2, ntf = 2, tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0, nstlim = 40000, dt = 0.002, ntpr = 40000,
> ntwx = 40000, ntwr = 40000 ig = -1
> /
> Keep Protein + DNA fixed with weak restraints
> 0.5
> RES 1 153
> END
> END
>
>
>
> --complex: 200ps of MD
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 10.0, ntr = 0, ig = -1,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 100000, dt = 0.002,
> ntpr = 100000, ntwx = 10000, ntwr = 100000
> /
>
>
>
>
>
> Sincerely,
>
> *Syeda Amna Arshi*
>
> *Ph.D. Scholar*
>
> Multidisciplinary Centre For Advanced Research and Studies
>
> Jamia Millia Islamia
>
> Delhi-110025
>
> Ph.no: 7737638065
>
>
> [image: Image result for save world by plant][image: Image result for
> save world by plant white background]
>
--
Sincerely,
*Syeda Amna Arshi*
*Ph.D. Scholar*
Multidisciplinary Centre For Advanced Research and Studies
Jamia Millia Islamia
Delhi-110025
Ph.no: 7737638065
[image: Image result for save world by plant][image: Image result for save
world by plant white background]
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Received on Wed Dec 23 2020 - 23:00:02 PST
