Hi,
On Wed, Nov 14, 2018 at 7:14 AM Rajarshi Roy <phd1701171011.iiti.ac.in> wrote:
> Warning: Replica# found lower than file specified with trajin.
> Warning: Found "remd_glycanD.mdcrd.001"; 'trajin remdtraj' requires
> lowest # replica.
This warning is letting you know what is going wrong. By default, the
way 'trajin remdtraj' is supposed to work is you specify the "lowest"
member of the ensemble (in this case its remd_glycanD.mdcrd.001 as
evidenced by the fact that you don't see the warning for this file)
and cpptraj searches for the rest based on file name numerical suffix.
This is all detailed in the 'trajin' entry in the cpptraj part of the
Amber manual - there is even a subsection dedicated to replica
trajectory processing.
So to summarize, you don't need to 'trajin' each individual member of
the ensemble, just the lowest one.
-Dan
> Found 71 replicas.
> Reading 'remd_glycanD.mdcrd.002' as Amber NetCDF
> [trajin remd_glycanD.mdcrd.003 remdtraj remdtrajtemp 300.00]
> Warning: Replica# found lower than file specified with trajin.
> Warning: Found "remd_glycanD.mdcrd.002"; 'trajin remdtraj' requires
> lowest # replica.
> Found 70 replicas.
> Reading 'remd_glycanD.mdcrd.003' as Amber NetCDF
> [trajin remd_glycanD.mdcrd.004 remdtraj remdtrajtemp 300.00]
> Warning: Replica# found lower than file specified with trajin.
> Warning: Found "remd_glycanD.mdcrd.003"; 'trajin remdtraj' requires
> lowest # replica.
> Found 69 replicas.
> Reading 'remd_glycanD.mdcrd.004' as Amber NetCDF
> .....................
> 1. Why replica number is reducing in each step?
> ....
> Target replica not found. Check that all replica trajectories
> Error: were found and that the target temperature or indices are valid
> Error: for this ensemble.
> ....
> 2. Why amber is asking for all the replica as I already upload all the
> replicas?
> I also attached my input file.
> Please help me out from this problem. As I am new in the replica exchange
> md simulation so it is very difficult for me to understanding the error and
> debug it .
> Thank you in advance!
> --
> *with regards*
>
> *Rajarshi Roy*
>
>
> *PhD Research Scholar*
>
> *Biosciences and Biomedical Engineering*
>
> *Indian Institute of Technology, Indore*
> *India*
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Received on Wed Nov 14 2018 - 06:30:03 PST
