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Corsol output file
#36593 09/21/17 07:40 PM
Joined: Jul 2017
Posts: 22
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Dear communities,
Recently I am calculate the residence time of molecules around a specific atom, but I don't know the meaning of contents in the output file. My script is as follows:
! setup images and nonbonded options
crystal define orth 64.3 52.8 53.6 90 90 90
crystal build cutoff 14 nope
image byres xcen 0.0 ycen 0.0 zcen 0.0 sele resn tip3 end
image byseg xcen 0.0 ycen 0.0 zcen 0.0 sele segid O* end

NBOND atom fshift cdie vdw vswitch -
ctonnb 10 ctofnb 12 cutnb 14

shake bonh para
faster on

label noimage
! set up shell
shell nshl 1 shthk 1 -
solute sele samhead end -
solvent sele resname TIP3 .and. type OH2 end

! calculate the SATM series for all water oxygens and
! sum up the correlation functions
corsol maxseries 1 maxtimesteps 2500 maxatom 10000 noup
enter AAAA satm shel 1 sele atom W* * OH2 end
traj firstu 51 nunit 2 begin 15000000 stop -
20000000 skip 2000
write AAAA unit 11 dumb time

And my output file is as follows:
TIME RESIDENT
# and 5181 secondary atoms
0.000000000 4.952019192
4.000000000 0.2460000000
8.000000000 0.1036414566
12.00000000 0.7285828663E-01
16.00000000 0.4765718863E-01
20.00000000 0.4286858974E-01
24.00000000 0.3366733467E-01
28.00000000 0.2285485164E-01
32.00000000 0.2206177296E-01
36.00000000 0.1404494382E-01
40.00000000 0.1525491770E-01
44.00000000 0.1164658635E-01
48.00000000 0.1044596223E-01
52.00000000 0.1688102894E-01
56.00000000 0.1769199839E-01
60.00000000 0.1287208367E-01
64.00000000 0.1488933602E-01
68.00000000 0.1006441224E-01
72.00000000 0.1329037455E-01
76.00000000 0.1087832393E-01
80.00000000 0.1209189843E-01
84.00000000 0.9677419355E-02
88.00000000 0.7260992336E-02
92.00000000 0.8474576271E-02
96.00000000 0.7670569237E-02
100.0000000 0.8885298869E-02
104.0000000 0.7676767677E-02
108.0000000 0.9296685530E-02
112.0000000 0.8896077638E-02
116.0000000 0.9708737864E-02
120.0000000 0.7284500202E-02
124.0000000 0.6072874494E-02
128.0000000 0.8910490077E-02
132.0000000 0.6888168558E-02
136.0000000 0.7701661938E-02
140.0000000 0.8110300081E-02
144.0000000 0.5273833671E-02
148.0000000 0.5275974026E-02
152.0000000 0.7308160780E-02
156.0000000 0.5686433794E-02
160.0000000 0.7720438846E-02
164.0000000 0.6504065041E-02
168.0000000 0.8946726312E-02
172.0000000 0.3661513426E-02
176.0000000 0.8547008547E-02
180.0000000 0.7328990228E-02
184.0000000 0.7739307536E-02
188.0000000 0.4889975550E-02
192.0000000 0.4076640848E-02
196.0000000 0.7748776509E-02
What't the unit of the two columns in the output file.

Please instruct me. Thank you very much.


Yonglan Liu
University of Akron
Re: Corsol output file
Yonglan Liu #36595 09/21/17 08:46 PM
Joined: Sep 2003
Posts: 8,507
rmv Online Content
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Online Content
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Joined: Sep 2003
Posts: 8,507
The first column is time in ps, the second is a sum of correlation functions. From the SATM description in corsol.doc:

Enters a series analogous to the CORRel SATM series. For each
atom specified its presence in the specified shell (NOTE: SHELL must
be set up before CORSOL is called, see *note
reorient:(shell.doc)) will be recorded. The resulting
correlation function is the sum of the auto-correlation function for
each specified atom.
This resulting function can be used in the
determination of the mean residence time of atoms in a given shell.


Rick Venable
computational chemist


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