VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 13 2017 - 23:28:26 CST

HI,
  I would also affirm the suggestion that you do energy evaluations
using the Gromacs tools rather than mixing values obtained from VMD/NAMD
with simulations performed with Gromacs. To mix/match a simulation computed
by one with other tools for energy evaluation seems like inviting trouble
to me. I would hope that most differences would be very minor, but why
take any risk at all if you don't have to? I would think you would
want to compute energies using exactly the same force field and
parameters that were used for the simulation, but that's just my own opinion.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Jan 14, 2017 at 11:41:27AM +1300, Ashar Malik wrote:
> Hi,
>
> Your question doesn't give enough detail for someone to post a solution.
> Did you manage to successfully load the gro file and the trajectory file
> prior to running your analysis?
> How did you run your RMSD analysis? Did you do it using a script ? or the
> graphical user interface?
> Were any errors reported?
>
> Secondly::
>
> Protein - ligand interaction is a very broad term :: You first need to know
> how they interact, then go about quantifying that interaction.
> Electrostatics, VDW energies ? if you don't know how they interact then you
> need to exhaustively look at all possible details (non-bonded energies) to
> figure that out
>
> Binding energy has different methods :: you could do implicit solvent -
> like perhaps an approximation like GBSA?? or you can do something better
> like thermodynamic integration ?? These are your choices and multiple
> methods are present to calculate this.
>
> For energy calculations -- depending on what you want - I believe, in
> gromacs, you have to make use of index files with proper system labels to
> be able to compute energies between groups. If you want just a global
> measure of energies, they should be present in the log file. For details on
> energies - as that is an MD thing - which you computed from GROMACS perhaps
> you need to go to the GROMACS mailing list??? If you were using NAMD you
> could look into "NAMDenergy" or "measure energy". However that is not
> advisable since you ran your simulations uses a very different forcefield
> so energies should be computed using the same. I am not sure if these
> plugins support reading gromacs based parameters, I believe that one should
> stay consistent i.e. use NAMD for simulations using CHARMM based
> forcefields and then use the same for energy calculations. I think NAMD
> can run gromacs based simulations but I am not sure about energies
> calculation bit seperately once a trajectory has been created -- but having
> said that my knowledge on this subject is far from exhaustive.
>
> For calculating the number of hydrogen bonds you can use the plugin ::
> http://www.ks.uiuc.edu/Research/vmd/plugins/hbonds/
>
> I believe that GROMACS allows you to calculate most of the energies itself.
> Perhaps consulting its manual for energy calculation would be a good place
> to start.
>
>
> On Sat, Jan 14, 2017 at 10:44 AM, maria khan <mariabiochemist1_at_gmail.com>
> wrote:
>
> > Dear VMD users,,
> > i am a new user of VMD.
> > im analysing results of MD simulation done by Gromacs when i want to draw
> > the RMSD plot,,it gives an empty result showing no graph curve,,how it can
> > be solved..i attached the file that u may understand my problem.
> > SEcondly how i can calculate protein ligand interaction?
> > how i calculate binding energy?
> > How i calculate H-bod ?
> > Ptential energy.
> > Thanks in advance.
> > Maria khan.
> >
>
>
>
> --
> Best,
> /A 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/