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obtain the component frames from a trajectory
#38333 09/01/21 09:45 PM
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Dani Offline OP
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I am trying to obtain the component frames from a dcd production trajectory in charmm_45_lite, a task that
that I have performed successfuly with previous charmm versions.
In this case I obtain an error message (illegal seek in some fortran routine). I have attached a screen snapshot
of the error (see file error1), the input file (dcd2crd1.inp) and the output file (slurm_6492870.out) in a zipped directory.
Thanks in advance for your help,
Daniel Sussman Villaverde
USC, Spain

Attached Files
charmm.zip (191.32 KB, 177 downloads)
SHA1: 4bb2176cf1d73874a6f39894878ade0042a41cd1
Re: obtain the component frames from a trajectory
Dani #38334 09/01/21 10:44 PM
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rmv Online Content
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Check the trajectory file sizes; that error can indicate an incomplete trajectory file. You may also need to review the simulation output log that produced that file.


Rick Venable
computational chemist

Re: obtain the component frames from a trajectory
Dani #38335 09/02/21 10:48 AM
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You HAVE to run charmm using the explicit specification of the input file (ie, do not use stdin redirection "<") since most MPI implementations cannot handle a file rewind. The CHARMM GOTO command results in a rewind operation.

Try this:

charmm_45_lite -i dcd2crd.inp


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: obtain the component frames from a trajectory
lennart #38336 09/02/21 03:23 PM
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Dani Offline OP
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It works, thank you very much lennart


Moderated by  lennart, rmv 

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