what are you morphing? it's not really possible to help without a more
complete description of what you did, and the results at each step. we also
need to know how you are analyzing it. there are multiple trajectory
outputs- how are you viewing them? what exactly do you mean when you say it
does not work?
On Mon, May 23, 2011 at 1:46 PM, Buddhadev Maiti <chebm.langate.gsu.edu>wrote:
> Dear Amber Users,
> I am performing NEB calculation for DNA in explicit solvent (system
> looks like DNA+water+ions). I used all atoms of DNA in the mask and
> force constant 200 kcal/mol-Å^2. I generated 42 replicas using morph.tcl
> script with the linear interpolation of coordinates. I minimized energy
> for the 42 replicas is about 50ps. Then those 42 replicas used for NEB
> simulation from energy minimized conformations. The protocol for this
> NEB simulation, I used:
> 1. 500ps for increasing the temperature from 0K to 300K using NMR
> restraint
> 2. 2ns for heating the system at 300K
> 3. 500ps for decreasing the temperature from 300K to 0K using NMR
> restraint
> 4. 2ns production run at 0K
> 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 - 11:00:04 PDT
