[gmx-users] 轉寄: Problems about calculating binding energy

[b91602001 at ntu.edu.tw]

Hi everyone,
I try to  calculate binding energy between DNA and Drug
and have some questions about the g_energy results.
First, I use g_energy command and there are many options.
I think the binding energy= LJ(SR)+LJ(LR)+Col(SR)+ Col(reci.) (options
in g_energy)
However, I 'm calculating binding energy of two groups(DNA ,Drug) I
set in mdp files before MD,and there's no "Col(reci.) DNA DRUG" option
to choose. I would like to know how to calculating binding energy now.

Second, I check the handbook but am still not very clear about the
definitions of L-J(SR) and L-J(LR) between two energy groups I set.
What do (Short Range) and (Long Range) represent, respectively? Is
there a cutoff value between them? If it is true, how can I set the
cutoff value between my two energy groups?

Third, The L-J(LR) between my two energy groups is bigger than L-J(SR)
(Of course both LR &SR are negative). Is that reasonable?

I really appreciate you can answer my questions.
Thank you,


best reguards


YCL



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