2011/1/7 Justin A. Lemkul <jalem...@vt.edu>
>
>
> Qin Qiao wrote:
>>
>>
>> 2011/1/7 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
>>
>>
>>
>> Qin Qiao wrote:
>>
>>
>>
>> 2011/1/7 Justin A. Lemkul <jalem...@vt.edu
>> <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
>> <mailto:jalem...@vt.edu>>>
>>
>>
>>
>>
>> Qin Qiao wrote:
>>
>> Dear all,
>>
>> I came across a problem when I want to make the REMD
>> trajectories continuous.
>>
>> What I did:
>>
>> 1. 'demux.pl <http://demux.pl> <http://demux.pl>
>> <http://demux.pl> REMD_0.log' --to get the
>> 'replica_index.xvg'
>>
>>
>> 2. 'trjcat -f ../REMD_*.xtc -o resort.xtc -demux
>> ../replica_index.xvg'
>>
>> It seems smooth. But when I check the rmsd of the output
>> 0_resort.xtc, I found it's still discontinuous.. with big
>> jumps
>> about 0.5nm..! Could you help me to figure out what's wrong?
>> Thanks a lot.
>>
It has been solved. The reason is for the order of the xtc file in
trjcat. I should use -f ../REMD_?.xtc ../REMD_??.xtc to get the
correct order, or it will be mixed. Many thanks to Prof. Spoel!
>>
>> Have you properly accounted for periodicity effects?
>>
>> -Justin
>>
>>
>> It's the same after I remove periodicity by trjconv -pbc mol -ur
>> compact ...
>>
>>
>> One iteration of trjconv is not necessarily enough to produce a
>> properly imaged trajectory. What is going on in the trajectory when
>> these spikes are occurring?
>>
>> -Justin
>>
>> In VMD, it just seems to change to a different conformation...
>>
>
> Then it sounds like something has gone wrong with the demultiplexing. As for
> what that is, it's hard to say. Look into the .log file and resulting .xvg
> file (from demux.pl) to make sure that the proper exchanges were identified.
> Then try to determine from which replica that sudden change arose (i.e., in
> which of the original trajectories was that configuration present). Finding
> it should be relatively easy; just dump out the frames at that time point
> from each of the trajectories to see.
>
> For further troubleshooting, it would also be useful to know your Gromacs
> version, in case there is some sort of bug. It is too early to tell, though,
> where the problem lies.
>
> -Justin
>
>> Best,
>>
>> Qin
>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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