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

[Sundari]

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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