I infer that you are using ASCII coordinate files. If so, you might
analyze your trajectory files, globally, using "grep" as a starting point.
If you are fortunate with your atom counts, this command below might list
only your box coordinates, which end each of your trajectory frames:
grep '^ *[0-9.]* *[0-9.]* *[0-9.]*$' mdcrd
37.820 37.820 37.820
37.777 37.777 37.777
37.726 37.726 37.726
37.663 37.663 37.663
Piping that into "wc" will tive you a count of these frames, which might
be helpful as in:
grep '^ *[0-9.]* *[0-9.]* *[0-9.]*$' mdcrd | wc -l
If this does not explain the trouble, try cutting out each column of the
mdcrd file - and verifying that it is either blank or contains a
well-formed number.
cut -c1-8 < mdcrd > column1.txt
grep -Ev '^ *\-?[0-9]{1,5}?.[0-9]{3,3}?$' column11.txt
cut -c9-16 < mdcrd > column2.txt
grep -Ev '^ *\-?[0-9]{1,5}?.[0-9]{3,3}?$' column12.txt
etc. through column 8
The grep expression above means "zero or more spaces, followed by an
optional minus sign, followed by one to five digits, followed by a period
followed by three more digits followed by a linefeed. The "-v" means list
lines that DON'T follow this format.
Hope this helps your search for the source of the trouble.
Chris
> I am simulating bilayer sistem in water.
> I break my longer simulation period into smaller
> fractions where by each contain 1000 frames.
> At first I reimage the system so that all the waters
> are in the box using below code:
>
> trajin ../betaM_lyo_md02_0900.mdcrd.gz
> trajout betaM_lyo_md02_0900.mdcrd mdcrd
> center :1-256
> image center familiar
>
> the output of this run is as below.
>
> DDM DDM DDM DDM DDM DDM DDM DDM DDM DDM
> ...
> DDM DDM DDM DDM DDM DDM WAT WAT WAT WAT
> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
> ...
> WAT WAT WAT WAT WAT WAT WAT WAT
> Scanning Box
> Successfully completed readParm.
> PTRAJ: Processing input file...
> Input is from standard input
> PTRAJ: trajin ../betaM_lyo_md02_0900.mdcrd.gz
> PTRAJ: trajout betaM_lyo_md02_0900.mdcrd mdcrd
> PTRAJ: center :1-256
> Mask [:1-256] represents 20736 atoms
> PTRAJ: image center familiar
> Mask [*] represents 23832 atoms
> PTRAJ: Successfully read the input file.
> Coordinate processing will occur on 999 frames.
> Summary of I/O and actions follows:
> INPUT COORDINATE FILES
> File (../betaM_lyo_md02_0900.mdcrd.gz) is an AMBER
> trajectory (with box info) with 999 sets
> OUTPUT COORDINATE FILE
> File (betaM_lyo_md02_0900.mdcrd) is an AMBER
> trajectory (with box info)
> ACTIONS
> 1> CENTER to box center via center of geometry, atom
> selection follows :1-256
> 7> IMAGE familiar by molecule to box center using
> the center of mass, atom selection * (All atoms are
> selected)
> IMAGE familiar, center is at box center
>
> Processing AMBER trajectory file
> ../betaM_lyo_md02_0900.mdcrd.gz
> Set 1
> .................................................
> Set 50
> .................................................
> Set 100
> .................................................
> Set 150
> .................................................
> Set 200
> .................................................
> Set 250
> .................................................
> Set 300 .....................
>
> PTRAJ: Successfully read in 321 sets and processed
> 321 sets.
> Dumping accumulated results (if any)
> ***********************************************************
>
>
>
>
> Actually it supposed read 1000 frames, but it
> reads only 321 frames.
>
> When I check the mdcrd file for any characters such
> as (*) .. I can't find any thing like this.
>
> In one nanosecond simulation I have 10 files with
> each 1000 frames.
> But some files are not shwoing any message like this
> in output file, but some are showing message like
> this.
>
> I need help to overcome this problem.
>
> I also done simulation again and again few times.
> But the results are still the same.
>
> Any expert can help me?
> I really appreciate your help.
>
> Thank you.
>
> Vijay
>
>
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Received on Wed Dec 05 2007 - 06:07:23 PST
