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Cannot write flexible parameters?
#27097 04/11/11 11:12 AM
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Edo Offline OP
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Hi All,
I am trying to write out an ASCII parameter file in binary format. I use the flexible parameters option, in the charmm version c35b5. When I try to write out the binary param file I get the error:

***** LEVEL 0 WARNING FROM <PARWTR> *****
***** Cannot write flexible paramters (yet).
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5

Obviously this message indicates this version of CHARMM cannot write out a binary param file with flexible parameter formatting. I thought I'd post this and ask if anyone knows of a work around?

I need to shrink the size of this file as it is large and takes up a lot of bandwidth when I run replica exchange using the ascii parameter file.

Thanks for any suggestions,
Ed

Here is the script I use to try this write:
set out param_new
set prm param_old
set top top_file.top

prnlev 3
! read parameter and topology files
open unit 10 read form name @top
read rtf unit 10 card
close unit 10

open unit 10 read form name @prm
read param flex unit 10 card
close unit 10

open write unit 10 file name @out_binary.prm
write param flex file unit 10
close unit 10

Re: Cannot write flexible parameters?
Edo #27116 04/11/11 09:33 PM
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rmv Online Content
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If available (development sites only), one option might to be use the REPD code in c36a5; this would eliminate the need for many short runs to do replica exchange, which many ad hoc methods do. The initial files (RTF, PARAM, PSF, etc.) are read only once with the REPD code.

Otherwise, you best bet might be to create a subdir in /scratch or /tmp (site dependent) on each of the nodes in the job, which contains the files read repetitively. This would at least eliminate any overhead in reading data from a remote disk, e.g. an NFS file server.


Rick Venable
computational chemist

Re: Cannot write flexible parameters?
Edo #27122 04/12/11 03:57 AM
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I'm really not sure if you'd find this useful, but did you try MMTSB for replica exchange? You only need to read in the parameter file once for each replica, and the overhead is very insignificant.

Re: Cannot write flexible parameters?
apredeus #27124 04/12/11 09:30 AM
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Thanks Rick and Apredeus for the useful suggestions, I should really modify the replica exchange code I wrote to avoid this issue.


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