From: Maximilian Ebert (max.ebert_at_me.com)
Date: Fri Jun 04 2021 - 16:38:03 CDT
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 <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!pDAF--74IildTv1UlAQlsAQ3Bi_p55e0sWNSWHOILBijfi5RwBOBN_aoQTKNabMAyw$ <>
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
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