[gmx-users] To make continuous trj in REMD

[Justin A. Lemkul]

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> 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

> Best,
> 
> Qin
> 

-- 
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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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