CHARMM Development Project Forums CHARMM Community Script Archive lipid C-D order parameters using CORREL

If I keep the water, I get the same result:
SR2 0 0
SS2 0 0
SX2 0 0
SY2 0 0

What is to be done?

Find the clues in your output file.

OK, now for the final part, in the output file I get:

ORREL> ! use final mantime to set AVER, FLUC for output
CORREL> open write unit 1 card name cd@{C}.txt
Parameter: C -> "2"
At line 145 of file /home/themis/c39a2/source/util/parse.src (unit = 5, file = 'test.inp')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 1 with status "KEEP"
VOPEN> Attempting to open::cd2.txt::
OPNLGU> Unit 1 opened for WRITE access to cd2.txt

I think this is the clue, but how do I interpret it?

The Fortran runtime error message suggests some kind of problem with the file named test.inp; perhaps that file has become corrupted in some way. You have not provided enough information to say any more.

Here is the file test.inp, for 274 POPC lipids.(I made it following the example above, with a saved trajectory file for lipids without water and a psf file written in charm format.The number of atoms in trajectory file match those in psf ):

! the axial avg order parameter for an input C no. @C
! modified for C=C case; first file @FF last file @LF
! subdir @S


! Read initial data files
open unit 1 read form name top_all36_lipid.rtf
read rtf card unit 1
close unit 1
open unit 1 read form name par_all36_lipid.prm
read param card unit 1
close unit 1

! Read parameter file in command line

open read card unit 1 name popc.psf
read psf card unit 1
open read card unit 1 name popc.crd
read coor card unit 1

! number of lipids
set nl = 274
! number of files
calc n = 1

calc mxa @NL * 6 * 4
calc mxs 10 + @NL*2 * 4
calc mxt 2000 * @N

! unsaturation check; beta chain
set ub = 0
define unsat sele atom A 1 C2@C .and. chem CEL1 end
if ub lt ?NSEL set ub ?NSEL
! unsaturation check; gamma chain
set ug = 0
define unsat sele atom A 1 C3@C .and. chem CEL1 end
if ug lt ?NSEL set ug ?NSEL

correl maxtim @MXT maxa @MXA maxs @MXS
enter sr zero
if ub eq 0 enter ss dupl sr
enter sx dupl sr
if ug eq 0 enter sy dupl sr
set k 1
label elp
if ub eq 0 then
enter w@K vect z A @K H@{C}R A @K C2@C
enter a@K vect r A @K H@{C}R A @K C2@C
enter x@K vect z A @K H@{C}S A @K C2@C
enter b@K vect r A @K H@{C}S A @K C2@C
else
enter w@K vect z A @K H@{C}1 A @K C2@C
enter a@K vect r A @K H@{C}1 A @K C2@C
endif
if c gt 15 goto eskip
if ug eq 0 then
enter y@K vect z A @K H@{C}X A @K C3@C
enter c@K vect r A @K H@{C}X A @K C3@C
enter z@K vect z A @K H@{C}Y A @K C3@C
enter d@K vect r A @K H@{C}Y A @K C3@C
else
enter y@K vect z A @K H@{C}1 A @K C3@C
enter c@K vect r A @K H@{C}1 A @K C3@C
endif
label eskip
incr k by 1
if k le @NL goto elp

! OPEN FILES, FILL SERIES VIA TRAJ

open read unit 1 file name popclipidsnowater.dcd

! LOOP OVER LIPIDS; NORM, CALC SCD, ACCUM
set k 1
label clp
mantim w@K ratio a@K
mantim w@K squa
mantim w@K mult 1.5
mantim w@K shift -0.5
mantim sr add w@K
if ub eq 0 then
mantim x@K ratio b@K
mantim x@K squa
mantim x@K mult 1.5
mantim x@K shift -0.5
mantim ss add x@K
endif
if c gt 15 goto mskip
mantim y@K ratio c@K
mantim y@K squa
mantim y@K mult 1.5
mantim y@K shift -0.5
mantim sx add y@K
if ug eq 0 then
mantim z@K ratio d@K
mantim z@K squa
mantim z@K mult 1.5
mantim z@K shift -0.5
mantim sy add z@K
endif
label mskip
incr k by 1
if k le @NL goto clp

! use final mantime to set AVER, FLUC for output
open write unit 1 card name cd@{C}.txt
echu 1
mantim sr divi @NL
echo sr@C ?AVER ?FLUC
if ub eq 0 then
mantim ss divi @NL
echo ss@C ?AVER ?FLUC
endif
if c gt 15 goto oskip
mantim sx divi @NL
echo sx@C ?AVER ?FLUC
if ug eq 0 then
mantim sy divi @NL
echo sy@C ?AVER ?FLUC
endif
label oskip
close unit 1

I don't see any problems with the input; however, the error message suggests there are non-printing control characters present in the file. While one possibility for that is accidental file corruption, sometimes this can occur for files which have been edited on a Windows or Mac OS X machine and then transferred to a Linux machine to run CHARMM. Note that TAB characters are not allowed in CHARMM input scripts. You may need to consult with a local computer guru to help you with this.

One thing you can try is to make a new file by using a graphic cut-and-paste from the old file to a new file, using a text editor on the Linux system. In principle, this should not copy any non-printing characters which may be causing trouble.

OK, I fixed that error, but I still have results 0.
Here is a sample of the output:

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec FSHIft VATOm VFSWIt
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
with mode 5 found 106586 exclusions and 97544 interactions(1-4)
found 24112 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 10550403 ATOM PAIRS AND 0 GROUP PAIRS
== PRIMARY == SPACE FOR 15825624 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
15104476 ATOM PAIRS WERE FOUND FOR ATOM LIST
823754 GROUP PAIRS REQUIRED ATOM SEARCHES


CORREL> enter sr zero

CORREL> if ub eq 0 enter ss dupl sr
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> enter sx dupl sr

CORREL> if ug eq 0 enter sy dupl sr
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL>

CORREL> set k 1
Parameter: K <- "1"

CORREL> label elp

CORREL> if ub eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> enter w@K vect z A @K H@{C}R A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> enter a@K vect r A @K H@{C}R A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> enter x@K vect z A @K H@{C}S A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> enter b@K vect r A @K H@{C}S A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> else
Skip commands until next ENDIF

CORREL> if c gt 15 goto eskip





CORREL> ! LOOP OVER LIPIDS; NORM, CALC SCD, ACCUM
CORREL> set k 1
Parameter: K <- "1"

CORREL> label clp

CORREL> mantim w@K ratio a@K ! DIVIDE VECTOR Z BY R (z OF UNIT VECTOR)
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim w@K squa ! z**2
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim w@K mult 1.5 ! * 3/2
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim w@K shift -0.5 ! - 1/2
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim sr add w@K
Parameter: K -> "1"
NSER: 1
NAMES: SR
TOTALS: 0
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> if ub eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> mantim x@K ratio b@K
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim x@K squa
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim x@K mult 1.5
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim x@K shift -0.5
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim ss add x@K
Parameter: K -> "1"
NSER: 1
NAMES: SS
TOTALS: 0
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> endif

CORREL> if c gt 15 goto mskip
Comparing "2" and "15".
IF test evaluated as false. Skipping command

CORREL> mantim y@K ratio c@K
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim y@K squa
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim y@K mult 1.5
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim y@K shift -0.5
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim sx add y@K
Parameter: K -> "1"
NSER: 1
NAMES: SX
TOTALS: 0
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> if ug eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> mantim z@K ratio d@K
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim z@K squa
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim z@K mult 1.5
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim z@K shift -0.5
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim sy add z@K
Parameter: K -> "1"
NSER: 1
NAMES: SY
TOTALS: 0
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> endif

CORREL> label mskip

CORREL> incr k by 1
Parameter: K <- "2"

CORREL> if k le @NL goto clp
Parameter: NL -> "274"
Comparing "2" and "274".
IF test evaluated as true. Performing command



CORREL> ! use final mantime to set AVER, FLUC for output
CORREL> open write unit 1 card name cd@{C}.txt
Parameter: C -> "2"
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 1 with status "KEEP"
VOPEN> Attempting to open::cd2.txt::
OPNLGU> Unit 1 opened for WRITE access to cd2.txt

CORREL> echu 1

CORREL> mantim sr divi @NL
Parameter: NL -> "274"
NSER: 1
NAMES: SR
TOTALS: 0
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> echo sr@C ?AVER ?FLUC
Parameter: C -> "2"
RDCMND substituted energy or value "?AVER" to "0"
RDCMND substituted energy or value "?FLUC" to "0"

CORREL> if ub eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> mantim ss divi @NL
Parameter: NL -> "274"
NSER: 1
NAMES: SS
TOTALS: 0
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> echo ss@C ?AVER ?FLUC
Parameter: C -> "2"
RDCMND substituted energy or value "?AVER" to "0"
RDCMND substituted energy or value "?FLUC" to "0"

CORREL> endif

CORREL> if c gt 15 goto oskip

Why do I keep getting 0 results?

SR2 0 0
SS2 0 0
SX2 0 0
SY2 0 0

Please review the READ BEFORE POSTING guidelines for suggestions on the best way to post output logs.

It looks like you may have omitted the all-important TRAJ command, which actually reads the trajectory file(s) and fills the requested time series with data. The comments in the sample inputs are usually important, such as this one:

! OPEN FILES, FILL SERIES VIA TRAJ

I didn't ommit. In the script I listed above I included TRAJ command as:

! OPEN FILES, FILL SERIES VIA TRAJ
open read unit 1 file name popclipidsnowater.dcd

I have one file only, popclipidsnowater.dcd. What else should I include?

Also, in the output, I got no errors in opening the trajectory file:
CORREL> ! OPEN FILES, FILL SERIES VIA TRAJ
CORREL> open read unit 1 file name popclipidsnowater.dcd
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 1 with status "KEEP"
VOPEN> Attempting to open::popclipidsnowater.dcd::
OPNLGU> Unit 1 opened for READONLY access to popclipidsnowater.dcd

CORREL>


Thank you,