Have you tryed for backbone atom rmsd I think you should ckeck backbone atom
rmsd whether it is same or lower than this.
> Thank you all.
>
> Here is the rms plot for the first 100ps.
>
> trajin 100ps.mdcrd
> rms first mass out time 0.1 :1-200
> center :1-200
> image
> strip :WAT
> strip :Na+
>
>
>
> On Wed, Feb 16, 2011 at 2:49 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> > I've run 2ns simulation and plotted the potential energy and volume from
>> > the output file. They looked stable, however when I did the rmsd
>> analysis
>> > on the system referring to the first frame of the trajectory, the rmsd
>> > values increasing from 0.2 A up to more than 100 A.
>>
>> You didn't send your RMS plot, so we can't see how abruptly it jumps.
>>
>> If you are including waters in your measurement, this could
>> easily explain it, since waters are mobile.
>>
>> You should always fit the solute coordinates to a common set before
>> getting RMS, otherwise drift and rotation will lead to an
>> increase. Also, if one of a set of molecules has been translated across
>> the box due to iwrap=1, you will need to use ptraj's image cmd to avoid
>> and RMS jump from that.
>>
>> Bill
>>
>> _______________________________________________
>> 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
>
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 15 2011 - 22:00:03 PST
