Hi, Dear Amber users
I have some questions about the utility in ptraj which computes radial
distribution function.
I use this input command:
trajin dynamics.mdcrd
radial output 0.01 10 :WAT :FLU
(where FLU is fluorescein residue; the trajectories are computed with
a NPT simulation with periodic boundary conditions)
1) If I do not specify the atom in the residue mask, is RDF calculated
with respect to molecules' centers of mass?
2) What does represent the third column in the output files?
3) I do not put a specific command in order to perform trajectory
image, since I read that imaging of distances is performed. Is this
correct? Do I have to give ptraj a specific command to image
trajectories?
I will thank you in advance for your help.
Have a nice day!
Tommaso
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Received on Thu Oct 06 2011 - 03:00:03 PDT
