From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Fri Sep 03 2021 - 15:42:44 CDT
Is there a reason you are using the memopt version of NAMD? As Giacomo
said, the memopt version requires bincoordinates files. However, if you
are using CHARMM-GUI to build your system, I'm inclined to believe that
your system is smaller than the multiple-millions of atoms that might
make a memopt version of NAMD mandatory.
On 9/3/21 3:58 PM, oivalf_nix_at_REMOVE_yahoo.com wrote:
> Thank you Giacomo.
> However, I am using the CharmmGui output *.pdb and *.psf which are in
> text format.
> Is there a way to convert them to binary, in order to use it as input
> for namd 2.14??
> Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Giacomo Fiorin
> <giacomo.fiorin_at_gmail.com> escreveu:
> 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.
> On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix_at_REMOVE_yahoo.com
> <oivalf_nix_at_remove_yahoo.com <mailto:oivalf_nix_at_remove_yahoo.com>> wrote:
> 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: *** EXPERIMENTAL MEMORY OPTIMIZED VERSION ***
> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
> Info: for updates, documentation, and support information.
> 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: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxx
> Info: Built Wed Aug 11 15:56:56 -03 2021 by root on
> 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
-- Josh Vermaas vermaasj_at_msu.edu Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology Michigan State University https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!pLTmlRIWBK4k1zRwhYeeLura8z-OkuSvoPXFFCrs4EEKD85HLSwuFFgcFXRWrECidA$
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