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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 23 2011 - 11:00:03 PDT
