[gmx-users] mail about g_energy parameter

[vidhya sankar]

Dear justin thank you for your reply
                                    i used the following parameter in my mdp file 

cutoff-scheme            = Group
rlist                    = 0.9
coulombtype              = PME
rcoulomb                 = 0.9
rvdw                     = 1.4
rvdw                     = 1.4
When i do g_energy analysis  to find out  LJ-SR nad Lj-SR between  CYCLIPEPTIDE1  and CNT it shows the negative value  -311.9    and   -2.45122 


J-SR:CYCLIPEPTIDE1-CNT      -311.9        1.5    18.6465   -5.28722  (kJ/mol) LJ-LR:CYCLIPEPTIDE1-CNT    -2.45122      0.019   0.265088  0.0560281  (kJ/mol) LJ-SR:CYCLIPEPTIDE2-CNT    -312.105          3    19.4763   -5.26101  (kJ/mol)LJ-LR:CYCLIPEPTIDE2-CNT    -2.69093     0.0077  0.0788448  -0.045267  (kJ/mol)LJ-SR:CYCLIPEPTIDE3-CNT    -322.101       0.98    18.1122    7.01285  (kJ/mol)
LJ-LR:CYCLIPEPTIDE3-CNT    -2.41642      0.023   0.236337  0.0742594  (kJ/mol)


can i take LJ-LR parameter for analysing and discussion the problem ? .
Because My g_ dist analysis shows the Distance between selected groups is is greater than 3.7 nm This value is  less than 0.9 & 1.4 ( as described in Mdp file)