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 ----- 完成轉寄郵件 ----- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
