# [gmx-users] tabulated potential - problem

Justin Lemkul jalemkul at vt.edu
Mon Sep 7 19:20:31 CEST 2015

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On 9/7/15 1:04 PM, Liz Bell wrote:
> Sorry I did not know how to deal with the fact that I posted my question with a
> wrong topic.
> Thank you for your answer. But I do not really understand what you mean. My
> topology contains those things like
> bond, angle and dihedral terms:
> [ bonds ]
> ;ai   aj  bondTyp  n    k
>    1    2    8      1    1
>    2    3    8      2    1
> [ angles ]
> ;  ai     aj     ak    angleTyp  n    k
>      1    2        3       8      1    1
>      4    5        6       8      1    1
> [ dihedrals ]
> ;  ai    aj  ak   al  dihedralTyp  n    k
>      1    7   10   13      8        0    1
>     52   55   58    4      8        0    1
> but the gmx energy options to chose are only the common ones like  ... 6
> Potential        7  Kinetic-En.      8  Total-Energy  ...

It would be helpful if you posted the entire list of choices, rather than some
subset.  Perhaps bonded terms are off in the case of tabulated potentials, but
I've never seen such a thing happen.

> and furthermore this:
> LJ-SR:P_1-P_1
> Coul-SR:P_1-P_1
> which are the LJ/coulomb short range of my energy group P_1.
> 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
> visualise the potential engergy of specific bond types?

No, but you can calculate it by measuring the distance between the atoms of
interest and applying whatever functional form you're using.

-Justin

> The potential energy of my system grows further until the system crashes.
> Considering the simulation until it stops shows that there might be
> a problem with the bonded potential and therefore I wanted to compute this
> particular potential energy.
> Thank you,
> Liz
> *Gesendet:* Montag, 07. September 2015 um 18:37 Uhr
> *Von:* "Justin Lemkul" <jalemkul at vt.edu>
> *An:* gmx-users at gromacs.org
> *Betreff:* Re: [gmx-users] tabulated potential - problem
>
>
> On 9/7/15 12:14 PM, Liz Bell wrote:
>  > Dear all,
>  > Is there a possibility to plot the intramolecular energy terms?
>  > 3. of "Diagnosing an Unstable System" of the page
>  > http://www.gromacs.org/Documentation/Terminology/Blowing_Up
>  > sounds as if this is possible. Gmx energy only shows the interaction energys of
>  > the energy groups but not of the energy terms like
>  > angle or dihedrals....
>  > Any idea?
>
> Internal terms are always printed to the .edr file, irrespective of energygrps,
> because internal terms are not decomposed. If they aren't showing up in the
> list of options, that means there are no internals in the topology.
>
> -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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--
==================================================

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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