Dear Manisha,
from the form of your graph it seems to me that you maybe used the RMSD
values from the out-files from your simulation to obtain the raw list of
RMSD values: If you run a simple grep-command through multiple out-files
simultaneously using wildcards (*.out), you not only get the RMSD values
for each written trajectory step, but also the mean value and the
fluctuations value. The last two occur at the end of the out-file in the
same format and are thus found by the grep command as well. In that way,
you get for each out-file that resembles a part of your total trajectory
two additional values, the last one of which is a small one (fluctuations).
Since the graph minima in your plot seem equidistant (ca. every 100
frames) this could be an explanation.
The solution for this would be either to modify your grep command to
neglect the last two entries from *every* out-file, or (much better) use
cpptraj from the AmberTools to compute the RMSD value on your own.
Regards,
Anselm
On 12/14/2020 01:15 PM, Bill Ross wrote:
> 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]
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 15 2020 - 01:00:02 PST
