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#27242 04/18/11 06:09 PM
Joined: Feb 2011
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J
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J
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Hi,

Im trying to direct output to a separate file using iunit. the files are being creating but nothing is getting outputted into them. The output looks fine in the charmm.out file. Here is the relevant portion of my script:

open unit 15 write form name 003.contact/@clusterid.hbcontact.dat
open unit 16 write form name 003.contact/@clusterid.allcontact.dat

coor hbond ncutb 2.5 ncuta 120 select segid proa .and. type HN .or. type O end select segid prob .and. type HN .or. type O end -
firstu 13 nunit 1 begin @start stop @stop skip 5 iunit 15
coor contact ncutb 5 select segid proa end select segid prob end -
firstu 13 nunit 1 begin @start stop @stop skip 5 iunit 16

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rmv Online Content
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The VERBOSE keyword may be needed; I think the data written to IUNIT is not the same as that written to the log, but is much more detailed. Use OUTU (miscom.doc) to just divert the COOR HBOND log output to a file--

open unit 15 write form name 003.contact/@clusterid.hbcontact.dat
outu 15 ! begin output diversion
coor hbond ...
outu 6 ! end diversion, back to stdout unit


Rick Venable
computational chemist

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The data written to IUNIt in VERBose mode is just a long list of the start and end times, with identitites of the involved atoms/groups, of all hbond/contact/bridge events.
Note that the default criteria to define a hydrogen bond (r(H-A)< 2.4A and no angle cutoff) are perfectly fine (JACS 114:4028). The COOR HBONd command is not particularly fond of keywords NCUTA and NCUTB (very few commands/keywords in CHARMM are identical in the first 4 positions).
SKIP 5 is very frequent sampling...
Note also that the .AND. operation has higher priority than .OR., so this selection may not do what you want:
select segid proa .and. type HN .or. type O end

For COOR CONTact you probably want a longer cutoff than what is used for hydrogen bonds.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
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when i use outu mpi kills my program with

CHARMM> open unit 15 write form name @clusterid.ssec.dat
Parameter: CLUSTERID -> "1"
VOPEN> Attempting to open::1.ssec.dat::
OPNLGU> Unit 15 opened for WRITE access to 1.ssec.dat

CHARMM>

CHARMM> outu 15
[seawulf:27841] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 13

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nevermind- i needed a dash to continue on the next line. I didnt get the charmm error output until i commented out the outu line


Moderated by  lennart, rmv 

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