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)
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