Hi Daniel,
Yes, I know that. But when I am only trajin the first replica it is not
taking the other replica. Here is my output,
CPPTRAJ: Trajectory Analysis. V17.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 11/16/18 13:21:14
| Available memory: 12.299 GB
INPUT: Reading input from '300.in'
[parm complex_solv.prmtop]
Reading 'complex_solv.prmtop' as Amber Topology
Radius Set: H(N)-modified Bondi radii (mbondi2)
[trajin remd_glycanC.mdcrd.001 remdtraj remdtrajtemp 300.00]
Found 72 replicas.
Reading 'remd_glycanC.mdcrd.001' as Amber NetCDF
Warning: Box information present in topology but not in trajectory.
Warning: DISABLING BOX in topology 'complex_solv.prmtop'!
[trajout remd.300.00k.mdcrd nobox]
Warning: Format not specified and extension '.mdcrd' not recognized.
Defaulting to Amber Trajectory.
Writing 'remd.300.00k.mdcrd' as Amber Trajectory
---------- RUN BEGIN -------------------------------------------------
PARAMETER FILES (1 total):
0: complex_solv.prmtop, 11035 atoms, 3596 res, box: None, 3584 mol, 3582
solvent
INPUT TRAJECTORIES (1 total):
0: REMD trajectories (72 total), lowest replica 'remd_glycanC.mdcrd.001'
(reading 4400 of 4400)
Looking for frames at 300.00 K
Coordinate processing will occur on 4400 frames.
OUTPUT TRAJECTORIES (1 total):
'remd.300.00k.mdcrd' (4400 frames) is an AMBER trajectory no box info,
BEGIN TRAJECTORY PROCESSING:
----- remd_glycanC.mdcrd.001 (1-4400, 1) -----
0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete.
Read 4400 frames and processed 4400 frames.
TIME: Avg. throughput= 38.5894 frames / second.
ACTION OUTPUT:
RUN TIMING:
TIME: Init : 0.0002 s ( 0.00%)
TIME: Trajectory Process : 114.0209 s (100.00%)
TIME: Action Post : 0.0000 s ( 0.00%)
TIME: Analysis : 0.0000 s ( 0.00%)
TIME: Data File Write : 0.0000 s ( 0.00%)
TIME: Other : 0.0001 s ( 0.00%)
TIME: Run Total 114.0212 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 114.0711 seconds.
--------------------------------------------------------------------------------
To cite CPPTRAJ use:
Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for
Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem.
Theory Comput., 2013, 9 (7), pp 3084-3095.
Please comment on that and help me out. Thanks for your concern
On Wed, Nov 14, 2018 at 7:45 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Fri Nov 16 2018 - 00:30:01 PST
