From: Maximilian Ebert (max.ebert_at_me.com)
Date: Sat Jun 05 2021 - 07:55:19 CDT
Thanks everyone. That is super helpful. We could implement JS writing for systems over 1mio atoms, which would also be helpful to write out fully compliant coordinate files I guess. Since we have a native writer i would like to implement this as well. Do i need to go through the C code or is there a full spec of the file format somewhere?
Max
> On Jun 5, 2021, at 5:56 AM, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
> 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> 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> 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!uRefTsOJu_lE1cCqZFtx8q7ivz16yB9C6w-hEDWgEhBjYF9qWEEKh05gOTXIpNtclQ$
>>>>> 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
> https://urldefense.com/v3/__https://prl.natsci.msu.edu/people/faculty/josh-vermaas/__;!!DZ3fjg!uRefTsOJu_lE1cCqZFtx8q7ivz16yB9C6w-hEDWgEhBjYF9qWEEKh05gOTV_26L4cQ$
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