[gmx-users] To calculate temperture in a specific region

[Mark Abraham]

Hi,

Yes, you would need a dynamic selection, so that your geometric criterion
is implemented every time step that you want to average, and then somehow
cope with the fluctuating numbers of particles selected. gmx select can
create such a thing, but few other GROMACS tools can use it without you
doing some manual scripting.

Mark

On Wed, Sep 23, 2015 at 4:15 AM Krishna Mohan Gupta <chekmg at nus.edu.sg>
wrote:

> Thanks Mark,
>
> Actually, at a particular time I am able to calculate temperature in a
> region. But on taking average of few picosecond trajectory to minimize the
> statistical error, molecules exchange their location with surrounding
> region. Therefore, it is difficult to take average.
> Is there any way to handle to this type of situation ?
>
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
> Abraham
> Sent: Wednesday, September 23, 2015 3:12 AM
> To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] To calculate temperture in a specific region
>
> Hi,
>
> If you're after such a group-wise temperature at a single point in time,
> then you can e.g. use gmx select to make your selection, and then gmx traj
> to get the velocities for those atoms (if you recorded them from mdrun with
> nstvout).
>
> Mark
>
>
> On Tue, Sep 22, 2015 at 8:03 AM Krishna Mohan Gupta <chekmg at nus.edu.sg>
> wrote:
>
> > Dear Gromacs users,
> >
> > I need to calculate temperature of molecules in a particular region
> > after equilibration run (NVT or NPT) but during simulation molecules
> > will exchange from one region to another.
> >
> > Can anyone have any suggestion in this regards ?
> > Thanks.
> >
> > Krishna
> >
> >
> > ________________________________
> >
> > Important: This email is confidential and may be privileged. If you
> > are not the intended recipient, please delete it and notify us
> > immediately; you should not copy or use it for any purpose, nor
> > disclose its contents to any other person. Thank you.
> > --
> > 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.
>
> ________________________________
>
> Important: This email is confidential and may be privileged. If you are
> not the intended recipient, please delete it and notify us immediately; you
> should not copy or use it for any purpose, nor disclose its contents to any
> other person. Thank you.
> --
> 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.
>