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sorry, but all I got is zero
CORREL> read chg unit 12 dumb colum 2 skip 1 delta 0.2 offset -34.9
**** Warning **** The following extraneous characters were found while command processing in CORREL
SKIP 1 DELTA 0.2 OFFSET -34.9

NSER: 1
NAMES: CHG
TOTALS: 350
AVERAGE: 0.303590
FLUCT: 0.098488
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> mantime chg integ
NSER: 1
NAMES: CHG
TOTALS: 350
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> mantime chg integ
NSER: 1
NAMES: CHG
TOTALS: 350
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

any comments on that?
thank you very much

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rmv Offline OP
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I've had some trouble with using an 'edit-spec' with that READ command myself lately. An alternate approach for the first part is--

! DECLARE SERIES OF TYPE ZERO
enter chg zero
! SETUP TO MATCH Z DATA; SKIP*DELTA SHOULD BE THE BIN WIDTH
! OFFSET IS THE Z COORD OF THE FIRST DATA POINT
edit chg skip 1 delta 0.1 offset -36.0
! OPEN AND READ CHARGE FILE
open unit 1 read card name zchg.dat
read chg unit 1 dumb colu 2

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dear rick,

thank you very much.
I obtain an reasonable graph when I did integrate from z to +z. However, the result seemed wrong if I integrate from -z to z. do you have any suggestion to modify the input or only thing i can do is reorganize my data?

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rmv Offline OP
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The result depends on whether the integration starts from the middle of the bilayer or the middle of the water; the sign changes. The starting region for the integration should also be fairly flat, or else the integral will have an apparent slope.

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Opps! I did a mistake, I wanted to say that I got reasonable graph when I integrate from 0 to +z, but not from -z to 0.
I would expect a symmetric plot (from -z to 0 and from 0 to +z). And I also expect a fairly flat at the stating region before the slope appears, but i didnt get it (although the charge density show zero value at that region). Please find the enclosed picture. Any comment on that?
thank you very much

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Last edited by beginner; 06/26/08 09:56 AM.
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the plot for water indicates some errors when i integrate from 0 to -z

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rmv Offline OP
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For the slope problem, try shifting the starting point for the integration, perhaps by dropping a few initial points. I don't have much idea about the problem with the water. I've generally done the double integration using the -z to +z range.

Also, you need to average the charge density over many ns of data.

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wrt to the script that we discuss, it seemed to me that I need to make an integration separately, from 0 to +z and from 0 to -z.
if I did the double integration from -z to +z , I got a strength output as you can see from the attachment.

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Quote:

The script can be used to get the charge density, which can be saved to a file.






Dear rick, what is the unit of the y-axis in this case? is it coulomb/cubic angstrom or volt?

thank you

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rmv Offline OP
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From usage.doc--

The CHARMM system of units: AKMA.

CHARMM uses a distinct system of units, the AKMA system. I.e.
Angstroms, Kilocalories/Mole, Atomic mass units. All distances are
measured in Angstroms, energies in kcal/mole, mass in atomic mass units,
and charge is in units of electron charge.

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