[gmx-users] To make continuous trj in REMD
qiaoqin47 at gmail.com
Fri Jan 7 14:33:08 CET 2011
2011/1/7 Justin A. Lemkul <jalemkul at vt.edu>
> Qin Qiao wrote:
>> Dear all,
>> I came across a problem when I want to make the REMD trajectories
>> What I did:
>> 1. 'demux.pl <http://demux.pl> REMD_0.log' --to get the
>> 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?
It's the same after I remove periodicity by trjconv -pbc mol -ur compact ...
> 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
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