[gmx-users] problem with continuation of md

sarbani chattopadhyay sarbani_c84 at rediffmail.com
Wed Sep 10 14:10:32 CEST 2008

  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

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 
>>provided the previois trajectory file, energy file for this. However the continuation run 
>>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 
>>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 
>>point at which ended.
>How did you make this determination?
>>Can anyone suggest any reason for this?
>>Thanks in advance
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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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