[gmx-users] mail about g_energy parameter

[Justin Lemkul]

On 4/25/15 11:53 AM, vidhya sankar wrote:
> 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)
>

I already answered this question:

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096844.html

These are atom-atom interaction energies within those groups; g_dist gives you 
COM distances between the groups, so you can't correlate the two.

-Justin

-- 
==================================================

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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