[gmx-users] Doubt in nmol tool

[nidhi]

I want to to calculate Rg of whole protein in the simulation box at a time
not the individual chains.
And for this I have selected Rg for "C-alpha" atoms plus  "-nmol 3" .

Thank You,
Sundari

On Mon, Apr 8, 2019 at 2:50 PM Soham Sarkar <soham9038 at gmail.com> wrote:

> What do you want?
> Do you want to calculate the radius of gyration of the three chain at a
> time?
> If so then make a index of these protein chains together and calculate rg
> by selecting it. If not then calculate the chain's rg individually.
> -Soham
>
> On Mon, 8 Apr 2019, 2:36 pm Sundari, <sundi6170 at gmail.com> wrote:
>
> > Dear Gromacs users,
> >
> > Can anyone explain about -nmol (number of molecules ) option in gmx
> gyrate
> > tool. According to me I have 3 peptide chains in my simulation box and I
> am
> > using " -nmol  3".
> > Is it correct what I have used for this option?
> >
> > Regards
> > Sundari
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