<P>
It seems that the trajectory is discontinuous. The coordinates in the pdb file generated <BR>
from the trajectory files show that the model corresponding to 2ns in the 2ns.pdb(at the <BR>
last ) file is different from the model corresponding to 2ns in the 10ns(extended).pdb( at <BR>
the first)<BR>
<BR>
Sarbani<BR>
<BR>
<BR>
<BR>
<BR>
On Wed, 10 Sep 2008 Justin A.Lemkul wrote :<BR>
><BR>
><BR>
>sarbani chattopadhyay wrote:<BR>
>> The post 2ns run had crashed.<BR>
>><BR>
>>The commands were<BR>
>>tpbconv -f 2ns.trr -e 2ns.edr -s 2ns.tpr -extend 10000<BR>
>><BR>
>>When it crashed ,the command given was<BR>
>>tpbconv -f ext10ns.trr -s ext10ns.tpr -e ext10ns.edr -o leftrun.tpr<BR>
>><BR>
><BR>
>So what you're saying then is that the coordinates that were the output from the first part <BR>
(say, 2ns.gro) do not match those you find in ext10ns.tpr? How did you make that <BR>
determination? Is the trajectory discontinuous?<BR>
><BR>
>-Justin<BR>
><BR>
>><BR>
>>On Wed, 10 Sep 2008 Justin A.Lemkul wrote :<BR>
>> ><BR>
>> ><BR>
>> >sarbani chattopadhyay wrote:<BR>
>> >> Hi all,<BR>
>> >> I had used the "tpbconv" command to give continuation run on a 2ns <BR>
simulation. I<BR>
>>had<BR>
>> >>provided the previois trajectory file, energy file for this. However the continuation <BR>
run<BR>
>>had<BR>
>> >>crashed due to power failure and I again had to give a rerun on it.<BR>
>> >><BR>
>> ><BR>
>> >I'm confused. Which part crashed? Start --> 2 ns, or the post-2ns time frame?<BR>
>> ><BR>
>> >Please provide the exact commands you gave to tpbconv.<BR>
>> ><BR>
>> >>Everything seems to be working well but surprisingly I find that the coordinates of <BR>
the<BR>
>>atoms<BR>
>> >>at 2ns , as found at the end of the 2ns simulation and the coordinates of the atoms <BR>
at<BR>
>>2ns at<BR>
>> >>the start of the continuation run are different. This means that the run didn't start <BR>
from<BR>
>>the<BR>
>> >>point at which ended.<BR>
>> ><BR>
>> >How did you make this determination?<BR>
>> ><BR>
>> >-Justin<BR>
>> ><BR>
>> >><BR>
>> >>Can anyone suggest any reason for this?<BR>
>> >>Thanks in advance<BR>
>> >>Sarbani<BR>
>> >> >><BR>
>> >><BR>
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>> <BR>
>>------------------------------------------------------------------------<BR>
>> >><BR>
>> >>_______________________________________________<BR>
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>> >-- ========================================<BR>
>> ><BR>
>> >Justin A. Lemkul<BR>
>> >Graduate Research Assistant<BR>
>> >Department of Biochemistry<BR>
>> >Virginia Tech<BR>
>> >Blacksburg, VA<BR>
>> >jalemkul[at]vt.edu | (540) 231-9080<BR>
>> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
>> ><BR>
>> >========================================<BR>
>><BR>
>><BR>
>><BR>
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>><BR>
>>_______________________________________________<BR>
>>gmx-users mailing list gmx-users@gromacs.org<BR>
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><BR>
>-- ========================================<BR>
><BR>
>Justin A. Lemkul<BR>
>Graduate Research Assistant<BR>
>Department of Biochemistry<BR>
>Virginia Tech<BR>
>Blacksburg, VA<BR>
>jalemkul[at]vt.edu | (540) 231-9080<BR>
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
><BR>
>========================================<BR>
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