[gmx-users] To make continuous trj in REMD

[Qin Qiao]

2011/1/7 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> Qin Qiao wrote:
>
>>
>>
>> 2011/1/7 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at 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
>
> ========================================
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