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

[Krishna Mohan Gupta]

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
>
>
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