[gmx-users] Problem with box-type after the extension of simulation

[Amit Choubey]

On Wed, Nov 18, 2009 at 9:29 PM, sukesh chandra gain <sukesh at atc.tcs.com>wrote:

> Dear All,
> I started a protein simulation for 100ps with octahedron box. After
> completion of that run I visualized the protein at the centre of the
> octahedron box by using trjconv.
> Then I have extended the simulation for another 500 ps by using tpbconv.
> But now it is showing as cubic box when I see the result after using
> trajconv (additionally some part of the protein is out of the box).


This could only be a visualization glitch.
Try using trjconv options.

amit


> I do not have any clue how the box type has been changed or where could I
> go wrong.
> Please comment.
> Thank you,
> Cheers,
> Sukesh
>
> --
> Sukesh Chandra Gain
> TCS Innovation Labs
> Tata Consultancy Services Ltd.
> 'Deccan Park', Madhapur
> Hyderabad 500081
> Phone:  +91 40 6667 3572
>
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