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#14353 05/11/07 08:32 PM
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preeti Offline OP
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Hello,

I am using "c33b2" version and running a parallel job. The dcd file i write below dosen't seem to be okay. It is accepting the retsart file, but when I open in VMD the following dcd file, it gives error and says it's corrupted.

I never have had this problem before, e.g. when i used c32b1 version. How can i recover dcd files without re-running the dynamics?

please help,
preeti

open unit 10 write unform name "m0-dyna2.dcd"
OPEN UNIT 21 write card name "m0-dyna2.rest"
OPEN UNIT 31 read card name "m0-dyna1.rest"

shake fast bonh para
SCALAR FBETA SET 3.0 SELE ALL END

GBMV UPDATE 1
DYNA LANGVEIN LEAP restart NSTEP 100000 TIMESTEP 0.002 -
IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 200 INBFRQ 50 IMGFRQ -1 -
IHBFRQ 0 IUNREA 31 IUNWRI 21 IUNCRD 10 IUNVEL -1 KUNIT -1 -
NPRINT 100 NSAVC 100 NSAVV 0 -
ILBFRQ 1000 RBUFF 0.0 ISVFRQ 1000 -
FIRSTT 300.00 FINALT 300.0 TEMINC 0.0 TBATH 300.0 -
TWINDH 10.0 TWINDL -10.0 TSTRUC 300.0 -
IASORS 1 ISCVEL 0 IASVEL 1 ICHECW 1 -
atom switch cdie vdw vswitch -
ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb

gbmv clear

Last edited by preeti; 05/11/07 08:35 PM.
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rmv Online Content
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There can be such issues related to the OS (e.g. i386 vs. x86_64) and the specific compiler used for CHARMM. The first test is to see if CHARMM can read the trajectory file; if so, it is not corrupted, but may not be fully compatible with your VMD version for several reasons.

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preeti Offline OP
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Rick,

It's the problem writing in charmm. It is for some reason just overwriting the dcd file. Instead of saving all the coordinates just saves one(the last one). But the same input file runs fine with c31b2 version and the dcd file is written correctly.

what do you suggest?

preeti

open unit 10 write file name "m0-dyna-gbmv.dcd"
OPEN UNIT 21 write card name "m0-dyna-gbmv.rest"
OPEN UNIT 31 read card name "m0-eq-gbmv.rest"

shake fast bonh tol 1.0e-8 para
SCALAR FBETA SET 10.0 SELE ALL END

GBMV UPDATE 1
DYNA LANGVEIN LEAP restart NSTEP 100000 TIMESTEP 0.002 -
IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 200 INBFRQ 50 IMGFRQ -1 -
IHBFRQ 0 IUNREA 31 IUNWRI 21 IUNCRD 10 IUNVEL -1 KUNIT -1 -
NPRINT 100 NSAVC 100 NSAVV 0 -
ILBFRQ 1000 RBUFF 0.0 ISVFRQ 1000 -
FIRSTT 300.00 FINALT 300.0 TEMINC 0.0 TBATH 300.0 -
TWINDH 10.0 TWINDL -10.0 TSTRUC 300.0 -
IASORS 1 ISCVEL 0 IASVEL 1 ICHECW 1 -
atom switch cdie vdw vswitch -
ctonnb @ctonnb ctofnb @ctofnb cutnb @cutnb

gbmv clear

Last edited by preeti; 05/13/07 07:22 AM.
Joined: Sep 2003
Posts: 8,629
Likes: 24
rmv Online Content
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I'm not aware of any other reports of a problem like that, and have not had any problems of that sort with c33b2 myself.

If you haven't already done so, run the c33b2 testcases, for both non-parallel and parallel compilations. It also sounds like you should do the same for your c31b2 executables as well.

The problems you are observing are unusual, and may indicate problems with the builds of the executables.

Last edited by rmv; 05/13/07 04:01 PM.

Moderated by  lennart, rmv 

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