Hi,
Without more information I don't think anyone would be able to help
you. It's not clear what you mean by 'drops in the rmsd', and why this
might be bad or something you don't expect. You'll have to at least
post what cpptraj input you're using as well, and maybe attach a
picture of a plot that illustrates the behavior you mention.
-Dan
On Thu, Dec 24, 2020 at 1:33 AM Syeda Amna Arshi
<seyydaamnaarshi.gmail.com> wrote:
>
> 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 30 2020 - 07:00:03 PST
