From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Sep 03 2021 - 19:05:43 CDT
Hi Flavio,
I think you misunderstand. NAMD 2.14 can be compiled with memopt turned either on or off. For 99% of users, memopt off is the correct version. Whoever compiled the module you are using needs to recompile it for turning memopt off (the default), or you can compile 2.14 yourself. I have streamlined instructions I keep handy for myself that lays out the process, https://urldefense.com/v3/__https://github.com/jvermaas/Software-Building-Instructions/blob/main/NAMD.md__;!!DZ3fjg!pc5iD9KMmOEOj0jB1WuKWx7HjCF6dMv8cj7L2dUbzVUnO6Q64CTmwSDWinFkHOb3BA$ . 2.14 is fine, but it’s the memopt part that is unneeded for your use case.
-Josh
From: "oivalf_nix_at_yahoo.com" <oivalf_nix_at_yahoo.com>
Reply-To: "oivalf_nix_at_yahoo.com" <oivalf_nix_at_yahoo.com>
Date: Friday, September 3, 2021 at 4:57 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Subject: Assunto: Re: namd-l: Binary coordinates NAMD 2.14
Thank you Josh
Our national computing laboratory aways uses the lastest version of the programs.
So, I will ask them to instal v2.12
Regards
Flavio
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Em sex., 3 3e set. 3e 2021 às 17:42, Josh Vermaas
<vermaasj_at_msu.edu> escreveu:
Hi Flavio,
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.
-Josh
On 9/3/21 3:58 PM, oivalf_nix_at_REMOVE_yahoo.com<mailto: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??
Regards,
Flavio
Em sexta-feira, 3 de setembro de 2021 16:43:02 BRT, Giacomo Fiorin <giacomo.fiorin_at_gmail.com><mailto: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.
Giacomo
On Fri, Sep 3, 2021 at 3:08 PM oivalf_nix_at_REMOVE_yahoo.com<mailto:oivalf_nix_at_REMOVE_yahoo.com> <oivalf_nix_at_remove_yahoo.com<mailto: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
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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<https://urldefense.com/v3/__http:/headnode.ada.cenapad.unicamp.br__;!!DZ3fjg!sYZsGGjJod27bxD8fYRwsxEdT0qix2X5kRIT7eZe02HbTfCd-Lkj0VtdkX6J0LYURg$>
Info: 1 NAMD 2.14 Linux-x86_64-MPI-memopt 128 adagp04 faseixas
Info: Running on 128 processors, 128 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 4.18685 s
Info: 8740.82 MB of memory in use based on /proc/self/stat
Info: Configuration file is ./input.conf
Info: Changed directory to .
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: fixedAtomsFile (fixedatoms)
Warning: fixedAtomsCol (fixedatoms)
FATAL ERROR: bincoordinates not found in the configuration file for the memory optimized version!
[Partition 0][Node 0] End of program
--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!pc5iD9KMmOEOj0jB1WuKWx7HjCF6dMv8cj7L2dUbzVUnO6Q64CTmwSDWinFp7cGv0w$