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Re: passing variables or file names from bash script to charmm
Rohit #37070 07/21/18 09:43 AM
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3/ VOPEN> Attempting to open::../output/0/unfold.job0.0.sort.dcd/::

as you can see there is a slash at end of dcd extension which causes error. other 2 methods doesn't add an extra slash at end.

why is happening ?
kindly help

Last edited by Rohit; 07/23/18 05:42 AM.
Re: passing variables or file names from bash script to charmm
Rohit #37071 07/21/18 08:32 PM
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It seems that this should only be used to specify the directory.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: passing variables or file names from bash script to charmm
Rohit #37072 07/22/18 08:24 AM
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Every thing works fine while recentring and orient but i get few error while opening log file.

Bash file
Code:
for j in {0..1}
do
	charmm i=$j -i recenter_orient.inp > recenter_orient$j.out
done


charmm script
Code:
open unit 61 write file name ./../anal/recen/@i/unfold_1le0.job0.@i.recen.dcd


warning's
Code:
 CHARMM>    TRAJ READ

 READING TRAJECTORY FROM UNIT  51
   NUMBER OF COORDINATE SETS IN FILE:        4000
   NUMBER OF PREVIOUS DYNAMICS STEPS:           0
   FREQUENCY FOR SAVING COORDINATES:            1
   NUMBER OF STEPS FOR CREATION RUN:         4000

 TITLE>  Created by DCD plugin\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00
 TITLE>  REMARKS Created 16 July, 2018 at 13:13\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\00\FF\FF\FF\FF\00\00\00
 TITLE>  *

Re: passing variables or file names from bash script to charmm
Rohit #37073 07/22/18 03:38 PM
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It appears you are using programs other than CHARMM in your workflow.

Programs written in C (or C++) cause this, as they pad strings with the NULL char, which prints as \00 and which Fortran (CHARMM) treats as text data. For these programs to have better CHARMM compatibility, the strings could be padded with blanks.


Rick Venable
computational chemist

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