Yes. I understand this. But my question is, if it is taking all the mdcrd
files, it should shows in the terminal that it is reading all of them. Here
is the output of my terminal,
====================================================
PPTRAJ: Trajectory Analysis. V17.00
___ ___ ___ ___
| \/ | \/ | \/ |
_|_/\_|_/\_|_/\_|_
| Date/time: 11/24/18 23:03:57
| Available memory: 2.327 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= 21.9377 frames / second.
ACTION OUTPUT:
RUN TIMING:
TIME: Init : 0.0001 s ( 0.00%)
TIME: Trajectory Process : 200.5683 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 : 0.0002 s ( 0.00%)
TIME: Run Total 200.5686 s
---------- RUN END ---------------------------------------------------
TIME: Total execution time: 201.4527 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.
===============================================================
You can check the *begin trajectory section,* only one trajectory is
showing. This is my only query. I think only one mdcrd was processing here
and the other replicas were remain unprocessed. Can you please help me to
solve this problem ?
Thank you for your concern.
On Mon, Nov 19, 2018 at 8:05 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Fri, Nov 16, 2018 at 12:47 PM Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
> > In the output, it shows that only 4400 frames were processed. That's why
> I
> > am asking. My every mdcrd file contains 4400 frames. My question is that
> If
> > is it processing all the replica then why it reads only 4400 frames?
> > Maybe I am missing something; please help me out.
> > Thank you again for your concern.
>
> During temperature replica exchange you have N replicas, each at a
> different temperature. Assuming no duplicate temperatures (which isn't
> allowed by Amber anyway), that means that at any given timestep there
> is only one replica at 300 K. So even though you have 72 replicas *
> 4400 frames, there are only 4400 frames at 300 K. Hope that helps,
>
> -Dan
>
> _______________________________________________
> 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*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 24 2018 - 10:00:02 PST
