[gmx-users] Regarding MM/GBSA method implemented in the GROMACS package

[rose rahmani]

As far as i know NO.
You want the adsorption energy which needs an accurate sampling of protein
in different distances and calculating energy for each sample and then ....
BTW, i think calculating this quantity for a big molecule like protein is
not a great idea. I think you need to do long time simulation and then find
out which residue/s are closer to nanotube most of the time and calculate
interaction energy or for more real adsorption energy cut that residue/s
and use umbrella sampling...

Rose



On Sat, 29 Sep 2018, 10:27 Sundari, <sundi6170 at gmail.com> wrote:

> Hi,
> Is there any  other way for example calculation of binding energy by my
> existed files (normal MD .trr and .edr files) generated by gromacs  instead
> of restart a simulation. Because currently  I am not familiar with the
>  umbrella sampling and have urgent need of energies.
> Please suggest any idea.
>
> sundari
>
>
>
>
> On Fri, Sep 28, 2018 at 8:47 PM rose rahmani <rose.rhmn93 at gmail.com>
> wrote:
>
> > Hi,
> >
> > You can calculate adsorption energy by umbrella sampling.
> > http://www.mdtutorials.com/gmx/umbrella/index.html
> > .edr just gives you the interaction energy not adsorption energy and
> > distance.
> >
> > Rose
> >
> > On Fri, Sep 28, 2018 at 6:37 PM Sundari <sundi6170 at gmail.com> wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I want to calculate Binding energy between the protein and the carbon
> > nano
> > > tube. Is there any way  to do that by gromacs commands.
> > >  As I only have .xtc and .tpr files from gromacs.
> > >
> > > Please suggest me any idea or any article so that based on trajectories
> > > (xtc or trr) how one can get these binding energies.
> > >
> > > Regards,
> > > Sundar
> > > --
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