[gmx-users] problem with continuation of md

[sarbani chattopadhyay]

  It seems that the trajectory is discontinuous. The coordinates in the pdb file generated 
from  the trajectory files show that  the model corresponding to 2ns in the 2ns.pdb(at the 
last ) file is different from the model corresponding to 2ns in the 10ns(extended).pdb( at 
the first)

Sarbani




On Wed, 10 Sep 2008 Justin A.Lemkul wrote :
>
>
>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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>>  >>
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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
>
>========================================
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