From: Mihaela Drenscko (quo.physics_at_gmail.com)
Date: Wed Feb 18 2015 - 07:34:15 CST
Thank you,
Mihaela
On Wed, Feb 18, 2015 at 4:13 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:
> There are two NAMD options that control if restart files are ascii or
> binary:
>
>
>
> binaryoutput yes/no <-- controls the final restart set
>
> binaryrestart yes/no <-- controls the intermediate restart sets
>
>
>
> So as you are using the file *restart.coor you use a file controlled by
> “binaryrestart”. It assume that you have set binary restart to “no” so you
> would need to use
>
>
>
> coordinates
>
> velocities
>
>
>
> instead of:
>
>
>
> bincoordinates
>
> binvelocities
>
>
>
> You can check if your restart file is ascii or binary by simply doing “cat
> yourfile” and see if you can read the content. If it just cryptic than the
> file is binary and your problem is somewhere else. Maybe the file is
> corrupted and you may want to try the*.old restart files instead. If that
> also doesn’t work, you atom count is in fact different between psf and
> restarts and so will never work together.
>
>
>
> Norman Geist.
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Mihaela Drenscko
> *Sent:* Wednesday, February 18, 2015 2:00 AM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* namd-l: Incorrect atom count in binary file
>
>
>
> Hi,
>
> I was running several metadynamics simulations with pcl (polycaprolactone)
> monomers in water. I had no problem with lower number of monomers (such as
> 5, 10, 20, 30, 44), but with 58 monomers, the simulation stops, with the
> error:
>
> Info: Reading from binary file ./../pcl58waterequi50.out.restart.coor
> FATAL ERROR: Incorrect atom count in binary file
> ./../pcl58waterequi50.out.restart.coor
>
> What is the cause of it and how do I fix it?
>
> Thank you,
> Mihaela
>
>
>
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