Re: PSF file format

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jun 04 2021 - 13:56:06 CDT

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> 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!vEskiYZs4uWQTl-q6HIFaq3vUrz4LU7wgXThKKXY1Je_RzZ9at1d7ZNw_ZqE3Na-bg$
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>

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