[gmx-users] simulation_time[Nikita Bora]

[Ms. Nikita Bora]

Thanks Tsjerk

That was really a good explanation. And it helped me out a lot.
Still,I would like to know what are the standard values for these
parameters as somewhere rvdw=1 and somewhere rvdw=1.4 is used.

As earlier it was mentioned that with different force field different
value is used so is there any link where i can get to know the minimum cut
off values for these parameters and which value should be used for which
force field or condition

thanks
Nikita



 ---------------------------- Original Message ----------------------------
> Subject: Re: simulation_time
> From:    "Ms. Nikita Bora" <niki24 at tezu.ernet.in>
> Date:    Mon, May 16, 2016 9:42 am
> To:      niki24 at tezu.ernet.in
> --------------------------------------------------------------------------
>
> Respected Sir,
>
> Thanks for the reply. I would further like to know that according to this
> tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
> the rvdw=rcoulomb=1 is used for the protein while according to this
> tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/07_equil2.html)
> rvdw=rcoulomb=1.4 is used. why a different value for the simple protein
> and protein-ligand complex is used??
>

Different force fields, different settings.

-Justin

>


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