[gmx-users] To calculate temperture in a specific region
Krishna Mohan Gupta
chekmg at nus.edu.sg
Wed Sep 23 04:14:31 CEST 2015
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 ?
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
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).
On Tue, Sep 22, 2015 at 8:03 AM Krishna Mohan Gupta <chekmg at nus.edu.sg>
> 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 ?
> 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
> * 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.
More information about the gromacs.org_gmx-users