[gmx-users] problem with continuation of md

[Justin A. Lemkul]

sarbani chattopadhyay wrote:
>   The post 2ns run had crashed.
> 
> The commands were
> tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 10000
> 
> When it crashed ,the command given was
> tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr
> 

So what you're saying then is that the coordinates that were the output from the 
first part (say, 2ns.gro) do not match those you find in ext10ns.tpr?  How did 
you make that determination?  Is the trajectory discontinuous?

-Justin

> 
> On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
>  >
>  >
>  >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?
>  >
>  >-Justin
>  >
>  >>
>  >>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
>  >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================