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:
>>
>> 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> 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.
>>
>>
>> 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...
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> | (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
>
> ========================================
> --
> gmx-users mailing list gmx-users@gromacs.org
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