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<div>Sorry I did not know how to deal with the fact that I posted my question with a wrong topic.</div>
<div> </div>
<div>Thank you for your answer. But I do not really understand what you mean. My topology contains those things like</div>
<div>bond, angle and dihedral terms: </div>
<div> </div>
<div>[ bonds ]<br/>
;ai aj bondTyp n k<br/>
1 2 8 1 1<br/>
2 3 8 2 1<br/>
[ angles ]<br/>
; ai aj ak angleTyp n k<br/>
1 2 3 8 1 1<br/>
4 5 6 8 1 1<br/>
[ dihedrals ]<br/>
; ai aj ak al dihedralTyp n k<br/>
1 7 10 13 8 0 1<br/>
52 55 58 4 8 0 1</div>
<div> </div>
<div>but the gmx energy options to chose are only the common ones like ... 6 Potential 7 Kinetic-En. 8 Total-Energy ...</div>
<div>and furthermore this:</div>
<div> </div>
<div>LJ-SR:P_1-P_1</div>
<div>Coul-SR:P_1-P_1</div>
<div> </div>
<div>which are the LJ/coulomb short range of my energy group P_1.</div>
<div> </div>
<div>But it is not possible to calculate the bonded energy between the specific bond ai and aj. Is it possible with any of the gromacs tools to</div>
<div>visualise the potential engergy of specific bond types?</div>
<div> </div>
<div>The potential energy of my system grows further until the system crashes. Considering the simulation until it stops shows that there might be</div>
<div>a problem with the bonded potential and therefore I wanted to compute this particular potential energy.</div>
<div> </div>
<div>Thank you,</div>
<div>Liz</div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 07. September 2015 um 18:37 Uhr<br/>
<b>Von:</b> "Justin Lemkul" <jalemkul@vt.edu><br/>
<b>An:</b> gmx-users@gromacs.org<br/>
<b>Betreff:</b> Re: [gmx-users] tabulated potential - problem</div>
<div name="quoted-content"><br/>
<br/>
On 9/7/15 12:14 PM, Liz Bell wrote:<br/>
> Dear all,<br/>
> Is there a possibility to plot the intramolecular energy terms?<br/>
> 3. of "Diagnosing an Unstable System" of the page<br/>
> <a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br/>
> sounds as if this is possible. Gmx energy only shows the interaction energys of<br/>
> the energy groups but not of the energy terms like<br/>
> angle or dihedrals....<br/>
> Any idea?<br/>
<br/>
Internal terms are always printed to the .edr file, irrespective of energygrps,<br/>
because internal terms are not decomposed. If they aren't showing up in the<br/>
list of options, that means there are no internals in the topology.<br/>
<br/>
-Justin<br/>
<br/>
--<br/>
==================================================<br/>
<br/>
Justin A. Lemkul, Ph.D.<br/>
Ruth L. Kirschstein NRSA Postdoctoral Fellow<br/>
<br/>
Department of Pharmaceutical Sciences<br/>
School of Pharmacy<br/>
Health Sciences Facility II, Room 629<br/>
University of Maryland, Baltimore<br/>
20 Penn St.<br/>
Baltimore, MD 21201<br/>
<br/>
jalemkul@outerbanks.umaryland.edu | (410) 706-7441<br/>
<a href="http://mackerell.umaryland.edu/~jalemkul" target="_blank">http://mackerell.umaryland.edu/~jalemkul</a><br/>
<br/>
==================================================<br/>
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