Hi Maiti,
This sounds normal to me. What exactly were you expecting? - To see the individual structures you need to load the restart file with a prmtop representing just one image. This is explained in the NEB tutorial on the AMBER website.
Good luck,
Ross
> -----Original Message-----
> From: Buddhadev Maiti [mailto:chebm.langate.gsu.edu]
> Sent: Monday, May 23, 2011 10:14 AM
> To: amber.ambermd.org
> Subject: [AMBER] NEB calculation using amber 11
>
> Dear Amber Users,
> I am performing NEB calculation for DNA. I used all atoms in the mask
> and force constant 200 kcal/mol-Å^2. From the NEB simulation, the beats
> (replicas) are top of the each other. Could you please give reply, what
> will be the problem, it will be great help for me.
> Have a nice day,
> Thanks,
> Maiti
>
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Received on Mon May 23 2011 - 10:30:05 PDT
