[gmx-users] mail about g_energy parameter
jalemkul at vt.edu
Sat Apr 25 18:07:05 CEST 2015
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:
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 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
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