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ardie Offline OP
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Dear all,
I want to seperate a 1ns production MD into two steps. But I can't find the DCD (prod2.dcd) and restart (prod2.res) file in the scr folder in 2nd production MD. And there is only prod2.kun in scr folder without prod1.kun.

Here is the input cript. What's wrong with it?

!=====================================================
! production 500ps
!=====================================================

! 1st production run
open read formatted unit 12 name ./scr/equi.res
open write formatted unit 13 name ./scr/prod1.res
OPEN UNIT 14 WRITe UNFORMatted NAME ./scr/prod1.dcd
open write formatted unit 16 name ./scr/prod1.kun

dyna leap verlet restart nstep 500000 timestep 0.001 -
isvfrq 1000 iprfrq 1000 nprint 500 -
ichecw 0 ieqfrq 0 finalt 300 NSAVcrd 1000 -
iunrea 12 iunwri 13 iuncrd 14 -
inbfrq -1 KUNIT 16

close unit 12
close unit 13
close unit 14
close unit 16

! write coordinates
open write unit 20 card name ./coor/prod1.pdb
write coor pdb unit 20
* end 500ps production
*
close unit 20

open write unit 20 card name ./coor/prod1.crd
write coor card unit 20
* end 500ps production
*

!=====================================================
! production 2nd 500ps (1ns)
!=====================================================

! 2nd production run
open read formatted unit 12 name ./scr/prod1.res
open write formatted unit 13 name ./scr/prod2.res
OPEN UNIT 14 WRITe UNFORMatted NAME ./scr/prod2.dcd
open write formatted unit 16 name ./scr/prod2.kun

dyna leap verlet restart nstep 500000 timestep 0.001 -
isvfrq 1000 iprfrq 1000 nprint 500 -
ichecw 0 ieqfrq 0 finalt 300 NSAVcrd 1000 -
iunrea 12 iunwri 13 iuncrd 14 -
inbfrq -1 KUNIT 16

close unit 12
close unit 13
close unit 14
close unit 16

! write coordinates
open write unit 20 card name ./coor/prod2.pdb
write coor pdb unit 20
* end 1ns production
*
close unit 20

open write unit 20 card name ./coor/prod2.crd
write coor card unit 20
* end 1ns production
*

stop

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ardie Offline OP
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no answer?

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rmv Online Content
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Nothing obvious in the output; check the output log for hints or clues.

It should be noted that setting ISVFRQ is no longer recommended; it's generally best to repeat a run, to keep all the files the same size to avoid complicated bookkeeping.


Rick Venable
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ardie Offline OP
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I check the output log but can't find any warning messages in it. Very strange.

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rmv Online Content
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What about normal messages? Are the file OPENs confirmed? Are there messages near the end of the dynamics that indicate a restart file is written, and that 500 coordinates sets have been saved?

It could be a filesystem problem.


Rick Venable
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ardie Offline OP
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Everything in the output seems normal because it is almost the same as the output by previous job. I can't find any clue.


Moderated by  lennart, rmv 

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