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Re: lipid C-D order parameters using CORREL
rmv #34467 10/05/14 09:56 PM
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The above only opens the file; look more closely at the original script.


Rick Venable
computational chemist

Re: lipid C-D order parameters using CORREL
rmv #34469 10/06/14 12:43 PM
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Mih Offline
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OK, this is the original script:
! OPEN FILES, FILL SERIES VIA TRAJ
set k = @FF
set u = 8
label opnlp
open read unit @U file name @S/dyn@K.trj
incr u by 1
incr k by 1
if k le @LF goto opnlp
traj firstu 8 nunit @N

I see here a loop to merge several trajectory files. In my case I don't have several trajectory file to merge. I have only one file, popclipidsnowater.dcd.
I don't see other command besides "open read unit @U file name @S/dyn@K.trj"

What am I missing?

Thank you,

Re: lipid C-D order parameters using CORREL
rmv #34470 10/06/14 03:50 PM
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There is no merge of several trajectory files. The loop simply opens the files ("connects the name to a unit number"). The actual reading of the file(s) is done withe the "traj firstu ..." command. What did you think this command was doing?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: lipid C-D order parameters using CORREL
rmv #34472 10/06/14 06:20 PM
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Since you're using a developer's version of CHARMM, there has to be someone in your institution who can help you answer all these basic questions.

Re: lipid C-D order parameters using CORREL
rmv #34474 10/06/14 11:07 PM
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What causes value 0 in fluctuation of order parameter?

Re: lipid C-D order parameters using CORREL
rmv #34475 10/06/14 11:45 PM
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Mih Offline
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I get all fluctuations as 0, starting like this:

TITLE> *
***** WARNING ***** BEGIN= 0 Was not specified. It has been set to: 0

1 CORD RECORDS READ FROM 1 UNITS STARTING WITH UNIT 1
RUNNING FROM STEP 0 TO 0 SKIPPING 1 STEPS BETWEEN RECORDS
Time step was 1.000000 AKMA time units.
1 Series "SR " Average = 0.000000 rms Fluctuation = 0.000000
2 Series "SS " Average = 0.000000 rms Fluctuation = 0.000000
3 Series "SX " Average = 0.000000 rms Fluctuation = 0.000000
4 Series "SY " Average = 0.000000 rms Fluctuation = 0.000000
5 Series "W1 " Average = -0.524498 rms Fluctuation = 0.000000
6 Series "A1 " Average = 1.110998 rms Fluctuation = 0.000000
7 Series "X1 " Average = -0.133732 rms Fluctuation = 0.000000
8 Series "B1 " Average = 1.111001 rms Fluctuation = 0.000000
9 Series "Y1 " Average = 0.705927 rms Fluctuation = 0.000000
10 Series "C1 " Average = 1.111002 rms Fluctuation = 0.000000
11 Series "Z1 " Average = -0.664016 rms Fluctuation = 0.000000

Why is that?

Re: lipid C-D order parameters using CORREL
rmv #34476 10/07/14 03:51 AM
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Mih Offline
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One more thing, just to be sure: I suppose I have to calculate an average between SR and SS and between SX and SY? (That in order to plot order parameter of each tail vs. carbon number).
Thank you,

Re: lipid C-D order parameters using CORREL
rmv #34477 10/07/14 04:10 AM
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The fluctuations are 0.0 because you've only read one frame. The script was written to analyze an ensemble of thousands of frames.

The averages are computed in the script and written to the output file.

These really are very, very basic questions that you should be discussing with others in your lab rather than posting here.


Rick Venable
computational chemist

Re: lipid C-D order parameters using CORREL
rmv #34478 10/07/14 11:40 AM
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Mih Offline
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In which way I specified reading one frame only and how can I correct that?

Thank you,

Last edited by Mih; 10/09/14 09:12 PM.
Re: lipid C-D order parameters using CORREL
rmv #34479 10/07/14 03:27 PM
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