On 4/22/15 4:10 AM, vidhya sankar wrote:
Dear Justin Thank you for your previous reply
When i run the g_energy tool to find out LJ-SR
nad Lj-SR between CYCLIPEPTIDE1 anf CNT it shows the negative value -311.9
and -2.45122 wha is the meaning of this Negative Value?If LJ-SR > LJ-LR
then
will it reperesent dominance of Vaderwall's replusive force ?
Negative energy means net attraction/favorable. Refer to a basic physics text
if this isn't apparent. The comparison between LJ-SR and LJ-LR really doesn't
make sense. The division of these terms simply means you used a twin-range
cutoff scheme. LJ-LR will inherently have a smaller magnitude because (1) the
interactions occur at longer distance and (2) there are fewer of these than
occur within the shorter cutoff.
-Justin
Could you please clarrify this little bit?
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
LJ-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)
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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