From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Sep 03 2021 - 14:20:57 CDT
By switching to the memory optimized version you commit to using binary
coordinates/velocities files. Using PDBs as restart files is never a good
idea for systems of any size, but for large systems the chances that you
run into the PDB format's range limitations become dangerously high.
Giacomo
On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix_at_REMOVE_yahoo.com <
oivalf_nix_at_remove_yahoo.com> wrote:
> Hi.
>
> I upgrade to NAMD 2.14 and foind the following problem:
>
> Does v2.14 use only binary files???
>
> Info: NAMD 2.14 for Linux-x86_64-MPI-memopt
> Warning:
> Warning: *** EXPERIMENTAL MEMORY OPTIMIZED VERSION ***
> Warning:
> Info:
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> Info:
> Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020)
> doi:10.1063/5.0014475
> Info: in all publications reporting results obtained with NAMD.
> Info:
> Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx
> Info: Built Wed Aug 11 15:56:56 -03 2021 by root on
> headnode.ada.cenapad.unicamp.br
> Info: 1 NAMD 2.14 Linux-x86_64-MPI-memopt 128 adagp04 faseixas
> Info: Running on 128 processors, 128 nodes, 1 physical nodes.
> Info: CPU topology information available.
> Info: Charm++/Converse parallel runtime startup completed at 4.18685 s
> Info: 8740.82 MB of memory in use based on /proc/self/stat
> Info: Configuration file is ./input.conf
> Info: Changed directory to .
> TCL: Suspending until startup complete.
> Warning: The following variables were set in the
> Warning: configuration file but will be ignored:
> Warning: fixedAtomsFile (fixedatoms)
> Warning: fixedAtomsCol (fixedatoms)
> FATAL ERROR: bincoordinates not found in the configuration file for the
> memory optimized version!
> [Partition 0][Node 0] End of program
>
>
>
>
> Enviado do Yahoo Mail no Android
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