That does seem strange. It’s hard to tell what might be going on from this
limited input and output. To try to debug this further, can you post your
entire cpptraj input (or the entire run script if the $i variables are
script variables) as well as the entire cpptraj output? Thanks.
-Dan
On Mon, Feb 16, 2026 at 9:56 AM Dulal Mondal via AMBER <amber.ambermd.org>
wrote:
> Dear Experts,
>
> I perform H+pH remd. (4 H replica + 6 pH replica), Total 24 replicas.
> 6 pH are 5 5.5 6 6.5 7 7.5
>
> I use ensemble commands like
>
> ensemble ../../001/nc.rep.$i trajnames
>
> ../../002/nc.rep.$i,../../003/nc.rep.$i,../../004/nc.rep.$i,../../005/nc.rep.$i,../../006/nc.rep.$i,../../007/nc.rep.$i,../../008/nc.rep.$i,../../009/nc.rep.$i,../../010/nc.rep.$i,../../011/nc.rep.$i,../../012/nc.rep.$i,../../013/nc.rep.$i,../../014/nc.rep.$i,../../015/nc.rep.$i,../../016/nc.rep.$i,../../017/nc.rep.$i,../../018/nc.rep.$i,../../019/nc.rep.$i,../../020/nc.rep.$i,../../021/nc.rep.$i,../../022/nc.rep.$i,../../023/nc.rep.$i,../../024/nc.rep.$i
> nstlim 2000 ntwx 1000
> trajout prod$i.nc netcdf
>
> This command generates 24 trajectory files from nane 0 to 23.
> like prod001.nc.0 ... prod001.nc.23.
>
> But when I use ncdump command to check the replica indices it shows:
>
> 1) ncdump -v remd_values prod001.nc.0 shows
>
> 0, 5,
> 2) ncdump -v remd_values prod001.nc.1 shows
> 0, 5.5
> 3) ncdump -v remd_values prod001.nc.5 shows
> 0, 7.5,
> but for ncdump -v remd_values prod001.nc.6 also shows 0, 5,
>
> trajin command also not work
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
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Received on Tue Feb 17 2026 - 03:30:02 PST
