[gmx-users] To make continuous trj in REMD

[Qin Qiao]

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
>> 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
>

It's the same after I remove periodicity by trjconv -pbc mol -ur compact ...


>  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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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