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<div>Thank you very much Justin.<br/>
I am going to do follow your recommendation and calculate the distance.</div>
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<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Montag, 07. September 2015 um 19:20 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>
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<br/>
On 9/7/15 1:04 PM, Liz Bell wrote:<br/>
> Sorry I did not know how to deal with the fact that I posted my question with a<br/>
> wrong topic.<br/>
> Thank you for your answer. But I do not really understand what you mean. My<br/>
> topology contains those things like<br/>
> bond, angle and dihedral terms:<br/>
> [ 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<br/>
> but the gmx energy options to chose are only the common ones like ... 6<br/>
> Potential 7 Kinetic-En. 8 Total-Energy ...<br/>
<br/>
It would be helpful if you posted the entire list of choices, rather than some<br/>
subset. Perhaps bonded terms are off in the case of tabulated potentials, but<br/>
I've never seen such a thing happen.<br/>
<br/>
> and furthermore this:<br/>
> LJ-SR:P_1-P_1<br/>
> Coul-SR:P_1-P_1<br/>
> which are the LJ/coulomb short range of my energy group P_1.<br/>
> But it is not possible to calculate the bonded energy between the specific bond<br/>
> ai and aj. Is it possible with any of the gromacs tools to<br/>
> visualise the potential engergy of specific bond types?<br/>
<br/>
No, but you can calculate it by measuring the distance between the atoms of<br/>
interest and applying whatever functional form you're using.<br/>
<br/>
-Justin<br/>
<br/>
> The potential energy of my system grows further until the system crashes.<br/>
> Considering the simulation until it stops shows that there might be<br/>
> a problem with the bonded potential and therefore I wanted to compute this<br/>
> particular potential energy.<br/>
> Thank you,<br/>
> Liz<br/>
> *Gesendet:* Montag, 07. September 2015 um 18:37 Uhr<br/>
> *Von:* "Justin Lemkul" <jalemkul@vt.edu><br/>
> *An:* gmx-users@gromacs.org<br/>
> *Betreff:* Re: [gmx-users] tabulated potential - problem<br/>
><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/>
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--<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/>
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