Are you rms-fitting the molecules? The details are important. I'd try
fitting DNA+protein, then fit and plot each alone.
Bill
On 12/14/20 1:16 AM, Manisha wrote:
> Hello,
> I am running simulation of a protein DNA complex, but the RMSD plot of the
> same shows fall in the RMSD value at equal intervals ( the straight lines)
> unlike only DNA that doesn't show such pattern of falling of values in
> RMSD. I am attaching the script of md_200ps.in as well as the rmsd plot.
>
> 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 = 1000, ntwr = 100000
> /
>
> Sincerely,
>
> *Manisha*
>
> *Ph.D. Scholar*
>
> Multidisciplinary Centre For Advanced Research and Studies
>
> Jamia Millia Islamia
>
> Delhi-110025
>
> Ph.no: 9518014737
>
>
> [image: Image result for save world by plant][image: Image result for save
> world by plant white background]
>
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Received on Mon Dec 14 2020 - 05:00:02 PST
