[gmx-users] Doubt in nmol tool

[nidhi]

Dhanyavad!!

On Mon, 8 Apr 2019, 16:34 Soham Sarkar, <soham9038 at gmail.com> wrote:

> No need to use -nmol
>
> On Mon, 8 Apr 2019, 4:21 pm nidhi, <nidhi020191 at gmail.com> wrote:
>
> > That means there is no need of using -nmol option.
> >
> > Thank You very much :)
> >
> >
> > On Mon, Apr 8, 2019 at 3:57 PM Soham Sarkar <soham9038 at gmail.com> wrote:
> >
> > > 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
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > >
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>