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