[gmx-users] problem with continuation of md

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 10 14:00:04 CEST 2008

sarbani chattopadhyay wrote:
>   Hi all,
>           I had used the "tpbconv" command to give continuation run on a 
> 2ns simulation. I had
> provided the previois trajectory file, energy file for this. However the 
> continuation run had
> crashed due to power failure and I again had to give a rerun on it.

I'm confused.  Which part crashed?  Start --> 2 ns, or the post-2ns time frame?

Please provide the exact commands you gave to tpbconv.

> Everything seems to be working well but surprisingly I find that the 
> coordinates of the atoms
> at 2ns , as found at the end of the 2ns simulation  and the coordinates 
> of the atoms at 2ns at
> the start of the continuation run are different. This means that the run 
> didn't start from the
> point at which ended.

How did you make this determination?


> Can anyone suggest any reason for this?
> Thanks in advance
> Sarbani
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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