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
___________________________________________________________
Support the World Aids Awareness campaign this month with Yahoo! For Good
http://uk.promotions.yahoo.com/forgood/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Dec 05 2007 - 06:07:12 PST
