Re: Binary coordinates NAMD 2.14

Date: Fri Sep 03 2021 - 14:58:55 CDT

 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 <> 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 <> 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-memoptWarning: Warning:        ***  EXPERIMENTAL MEMORY OPTIMIZED VERSION  ***Warning: Info: Info: Please visit for updates, documentation, and support information.Info: Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475Info: in all publications reporting results obtained with NAMD.Info: Info: Based on Charm++/Converse 61002 for mpi-linux-x86_64-mpicxxInfo: Built Wed Aug 11 15:56:56 -03 2021 by root on headnode.ada.cenapad.unicamp.brInfo: 1 NAMD  2.14  Linux-x86_64-MPI-memopt  128    adagp04  faseixasInfo: Running on 128 processors, 128 nodes, 1 physical nodes.Info: CPU topology information available.Info: Charm++/Converse parallel runtime startup completed at 4.18685 sInfo: 8740.82 MB of memory in use based on /proc/self/statInfo: Configuration file is ./input.confInfo: Changed directory to .TCL: Suspending until startup complete.Warning: The following variables were set in theWarning: 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

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