From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Sat Jun 05 2021 - 04:54:48 CDT
For the fortran style formatting, the VMD source code or the CHARMM source code. These are the lines from psfplugin.c:
Normal: "%8d %-4s %-4d %-4s %-4s %-4s %14.6g %13.6g %7d\n"
EXT: "%10d %-8s %-8d %-8s %-8s %-6s %14.6g %13.6g %7d\n"
The NAMD format just overruns the specified field widths, which is perfectly allowable in C but not in fortran.
In terms of using the js format, I think what you are seeing was more true when that warning was written (~2015, 2016), than it is now.
-Josh
On 6/4/21 5:38 PM, Maximilian Ebert wrote:
Hi Giacomo,
This is a bit concerning:
Due to the lack of full structure data on every node, various features not normally needed for large simulations are non-functional or restricted. These limits, combined with the small number of projects using memory-optimized NAMD, cause us to caution users that this capability should be considered experimental.
Also is there a full documentation of the JS and namdbin format? Where can I find the Fortran style formatting for PSFs? And how are they different when read into NAMD?
Max
On Jun 4, 2021, at 2:56 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com<mailto:giacomo.fiorin_at_gmail.com>> wrote:
Hi Max, for large systems the recommended format in VMD/NAMD is "JS":
https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction
On Fri, Jun 4, 2021 at 2:53 PM Maximilian Ebert <max.ebert_at_me.com<mailto:max.ebert_at_me.com>> wrote:
Thanks for the answer. I am trying to write out a compliment PSF file for system with over 1 million atoms. I want to be sure to not bust any field width and get into trouble with the NAMD PSF parser. So I guess you can’t be fully compliant for system which go over a certain number of atoms correct? Is my assumption correct that NAMD uses the space as a separator and that VMD for example has fixed field width?
Max
On Jun 4, 2021, at 1:59 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
lore has it that the *authoritative* documentation of the CHARMM file formats is the CHARMM source code.
one important point to note is that PSF (and PDB) are file formats based on Fortran style formatting, which has fixed widths and does not need spaces as separators.
so it can be legal to have something like:
1001100210031004 (for a 4I4 format) being read as 1001, 1002, 1003, 1004 but if you would write out 1001 1002 1003 1004 in would be read as 1001, 100, 210, 31
that is different from how C/C++ and Python process input.
So what it now boils down to is what you are after: do you want to write out or edit PSF files to be fully conforming, or do they just have to be read by NAMD.
Axel.
P.S.: there are some more possible flags to appear in the first line to indicate the use of the PSF for specific purposes
On Fri, Jun 4, 2021 at 1:49 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:
The best documentation on the format is *probably* the CHARMM
documentation, which is actually rather sparse.
https://urldefense.com/v3/__https://academiccharmm.org/documentation/version/c45b2/io*IOFORM__;Iw!!DZ3fjg!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxHM9_y3qw$
Basically, the first line of the PSF file dictates the field width. For
regular, non-extended PSFs, the header will look like:
PSF
In these files, you are limited to 4 characters for segnames and
atomtypes. CHARMM can also write (and VMD/NAMD can also read/write)
"extended" PSF files. The headers for these will look like:
PSF EXT
This buys you 8 characters for segnames and atomtypes. NAMD/VMD also can
write space-delimited psf files, which are tagged as follows:
PSF NAMD
The NAMD/VMD version is the most flexible, since fields just need to be
separated by spaces, and for the most part psfgen/VMD will select this
option if the contents of the psf file demand it.
-Josh
On 6/4/21 1:10 PM, Maximilian Ebert wrote:
> Dear list,
>
> Is there a resource which describes the PSF file format? I am many wondering about the max column width and if the width needs to be fixed or can changed when numbers get larger.
>
> Thanks
>
-- 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!uRPWqMKGW1780p7gOxom55ZPP9L4h9AHLa2pb7HsKx66nLOh7NH4vymgTxF1980Jig$ -- Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!tca8shL5MNjPvKe0WQ2CuKt_WzZHsbdeZOJRaXxyIaLAg4TDr1AklyLLa9o-tCCMkQ$ College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy. -- Josh Vermaas Assistant Professor, MSU-DOE Plant Research Lab and Department of Biochemisty and Molecular Biology vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!tca8shL5MNjPvKe0WQ2CuKt_WzZHsbdeZOJRaXxyIaLAg4TDr1AklyLLa9rskPyosA$
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