[gmx-users] To make continuous trj in REMD

[Justin A. Lemkul]

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.
> 
> 
>            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

========================================