[gmx-users] Doubt in nmol tool

[Soham Sarkar]

In that case select all c-alpha and make a group in index.ndx and run gmx
gyrate for this group only and you are done.

On Mon, 8 Apr 2019, 3:09 pm nidhi, <nidhi020191 at gmail.com> wrote:

> 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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