[gmx-users] mail About LJ obtained by g_energy

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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