[gmx-users] How to calculate interaction energy between two groups for every frame in a trajectory?
Justin Lemkul
jalemkul at vt.edu
Mon Aug 19 14:54:18 CEST 2019
On 8/19/19 7:44 AM, Sun Yeping wrote:
> Hello Justin,
>
> Thank you for your answer. I agree that the physical meaning of
> interaction energy is questionable. Actually, the structure with the
> lowest interaction energy between two groups in the trajectory is very
> different from what I expect.
>
> Then, how should I find a structure from a MD trajectory which is
> most possibly close to the real structure? I
Agreement with reality depends on the availability of data regarding the
biomolecule(s) in solution.
> think maybe I can select a real crystal structure related to the
> structure upon which the MD simulation was done, and use it as the
> reference structure, and calculate rmsd of each frame in the
> trajectory against the reference structure, and find the one with the
> smallest rmsd. But how to calculate the rmsd? The simulated structure
> has different atom number with the reference structure, so gmx rmsd
> wouldn't work. Do you know which method can work in this case?
RMSD to a crystal structure does not tell you anything about how
realistic your results are. Crystal environments are very different from
solution so RMSD doesn't tell you anything conclusive. I don't
understand why you don't have a matching reference structure - you had
to start your simulation from some known coordinates, no?
-Justin
>
> Best wishes.
>
> Yeping Sun
>
> On Mon, Aug 19, 2019 at 6:59 PM Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> On 8/18/19 11:28 PM, sunyeping wrote:
> > Hello Bratin Kumar Das，
> >
> > Your answer is correst but irrelevent to my question. By adding
> energygrps option in the mdp and rerun the trajectory and generate
> the edr file containing the interation energy information which
> can be extracted by enemat. However enemat only gives the range of
> the interaction energy. My question is how to calculate
> interaction energy between two groups for every frame in the
> trajectory.
>
> That is precisely what Bratin is telling you to do, and his answer is
> exactly correct.
>
> You need to use gmx energy, not gmx enemat, to get the interaction
> energy values in every frame. Then find the lowest and extract the
> corresponding frame with trjconv. Whether or not this quantity has
> any
> physical meaning is, however, questionable for most force fields.
>
> -Justin
>
> > ------------------------------------------------------------------
> > From:Bratin Kumar Das <177cy500.bratin at nitk.edu.in
> <mailto:177cy500.bratin at nitk.edu.in>>
> > Sent At:2019 Aug. 19 (Mon.) 11:11
> > To:gromacs <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>; 孙业平 <sunyeping at aliyun.com
> <mailto:sunyeping at aliyun.com>>
> > Subject:Re: [gmx-users] How to calculate interaction energy
> between two groups for every frame in a trajectory?
> >
> > You need to prepare one .mdp file where the energygrps = DNA
> Protein ( as example). Generate the .tpr file and rerun using
> mdrun module.
> > gmx mdrun -v -s new-tpr file -deffnm new -rerun me.xtc
> > On Mon 19 Aug, 2019, 8:09 AM sunyeping, <sunyeping at aliyun.com
> <mailto:sunyeping at aliyun.com>> wrote:
> > Dear all,
> >
> > I am doing protein-DNA complex simulations with gromacs and I
> have gotten a trajectory. Now I want to calculate interaction
> energy between the protein and the DNA in every frame of the
> trajectory so that I can pick out a frame in which the
> interaction energy between them is the largest, but I don't know
> how. I have used "enemat" , but it only gives a range of the
> energy, not every frame. The output read:
> >
> > Last energy frame read 5000 time 500000.000
> > Will build energy half-matrix of 2 groups, 6 elements, over
> 5001 frames
> > Matrix of Coul-SR energy ranges from -18999.681641 to -1608.268188
> > Matrix of LJ-SR energy ranges from -2540.941650 to -675.151306
> > Matrix of total energy ranges from -21540.623047 to -2283.419434
> >
> > So could you tell me how to calculate interaction energy
> between two groups for every frame in a trajectory?
> >
> > Best regards.
> > --
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu <mailto:jalemkul at vt.edu> | (540) 231-3129
> http://www.thelemkullab.com
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
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