Can you explain how your simulation directories are laid out? From this:
ensemble ../../001/nc.rep.001 trajnames ../../002/nc.rep.001,../../
003/nc.rep.001,../../004/nc.rep.001,
It looks like you are reading in the lowest coordinate trajectory from
multiple runs, which would make it not possible to properly sort. I.e. if
there is a ../../001/nc.rep.002, ../../001/nc.rep.003 etc, you aren’t using
‘ensemble’ in a way that you can sort by replica.
-Dan
On Tue, Feb 17, 2026 at 7:56 AM Dulal Mondal <
babunmondal.chem.kgpian.iitkgp.ac.in> wrote:
> Thank you sir for your response.
> The cpptraj input file is like
> parm ../../hcaii.prmtop
> ensemble ../../001/nc.rep.001 trajnames
> ../../002/nc.rep.001,../../003/nc.rep.001,../../004/nc.rep.001,../../005/nc.rep.001,../../006/nc.rep.001,../../007/nc.rep.001,../../008/nc.rep.001,../../009/nc.rep.001,../../010/nc.rep.001,../../011/nc.rep.001,../../012/nc.rep.001,../../013/nc.rep.001,../../014/nc.rep.001,../../015/nc.rep.001,../../016/nc.rep.001,../../017/nc.rep.001,../../018/nc.rep.001,../../019/nc.rep.001,../../020/nc.rep.001,../../021/nc.rep.001,../../022/nc.rep.001,../../023/nc.rep.001,../../024/nc.rep.001
> nstlim 2000 ntwx 1000
> trajout prod001.nc netcdf
> run
>
> *This input file works. *
> But When I check replica indices using the command
>
> *ncdump -v remd_values prod001.nc.0*
> *It shows * 0, 5
> ncdump -v remd_values prod001.nc.1
> 0, 5.5 ;
> It always shows 0 from 0 to 23.
>
> The output error like.
>
>
> My 2D remd (H+pH) like :
> hamiltonian.dat file
> HAMILTONIAN
> Hamiltonian Replica Exchange with different mdins
> 300
> 305
> 310
> 315
> and
> phs.dat file
> PH
> pH Replica Exchange
> 5.0
> 5.5
> 6.0
> 6.5
> 7.0
> 7.5
>
> and remd.dim.hphremd files:
>
> &multirem
> exch_type='HAMILTONIAN'
> group(1,:)=1,7,13,19,
> group(2,:)=2,8,14,20,
> group(3,:)=3,9,15,21,
> group(4,:)=4,10,16,22,
> group(5,:)=5,11,17,23,
> group(6,:)=6,12,18,24,
> desc='Hamiltonian Replica Exchange with different mdins'
> /
> &multirem
> exch_type='PH'
> group(1,:)=1,2,3,4,5,6,
> group(2,:)=7,8,9,10,11,12,
> group(3,:)=13,14,15,16,17,18,
> group(4,:)=19,20,21,22,23,24,
> desc='pH Replica Exchange'
> /
>
>
>
> On Tue, Feb 17, 2026 at 4:49 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> 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.*
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
> --
> *With regards,*
> *Dulal Mondal,*
> *Research Scholar,*
> *Department of Chemistry,*
> *IIT Kharagpur, Kharagpur 721302.*
>
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Received on Tue Feb 17 2026 - 13:30:02 PST
