From: Selemon Bekele (selemon_at_uakron.edu)
Date: Tue Mar 17 2020 - 14:51:04 CDT
Dear Lennart,
thank you so much for your prompt answer. I checked the numbers against the charges in the PSF file and it perfectly makes sense now. In my email I think I wrongly said "the the numbers in columns 1, 4 and 7 correspond to the last atoms in the groups in the rtf file." However, looking closely, because of the the first triplet (0 2 0), it seems indexing starts from 0, and those numbers correspond to the very first atoms in the groups:
27564 0 !NGRP NST2
0 2 0 14 1 0 32 1 0
44 1 0 58 1 0 70 2 0
84 1 0 97 1 0 109 1 0
.
.
.
Regards,
Selemon
________________________________
From: Lennart Nilsson <lennart.nilsson_at_ki.se>
Sent: Tuesday, March 17, 2020 1:46 PM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>; Selemon Bekele <selemon_at_uakron.edu>
Cc: Rajiv Berry <rajivpatch_at_gmail.com>
Subject: RE: NGRP NST2
Hi,
The PSF is an internal CHARMM data structure, which may for convenience only be stored in a file for later retrieval; many users prefer to regenerate the PSF each time it is needed since this does away with any uncertainty regarding the assumptions behind it. I am not very familiar with NAMD, so this may not be possible in NAMD. The file is a text file for portability reasons only - it is not intended to be read or manipulated by humans. The RTF and parameter files are what you should work with.
That said, the numbers in cols 2,3 (5,6 and 7,8) are flags indicating the type of the group and whether the whole group is fixed (frozen, not moving) , respectively:
! IGPTYP Groups Coded type of each group
! (0-no charges,1-neutral group,2-charged,3-ST2)
! IMOVEG Groups Used if entire group has fixed atoms
This may change in future versions of the CHARMM, although we are very conservative regarding such changes.
Best wishes,
Lennart Nilsson
Karolinska Institutet
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of Selemon Bekelemoveg
Sent: Tuesday, March 17, 2020 6:13 PM
To: namd-l_at_ks.uiuc.edu
Cc: Rajiv Berry <rajivpatch_at_gmail.com>
Subject: namd-l: NGRP NST2
Hi there,
I am trying to understand the meaning of the numbers under the "NGRP NST2" section of a PSF file. I have been searching the internet for clues but have not succeeded and am posting the issue to the list as a final resort.
The PSF file is for a simulation with the DRUDE model in NAMD.
27564 0 !NGRP NST2
0 2 0 14 1 0 32 1 0
44 1 0 58 1 0 70 2 0
84 1 0 97 1 0 109 1 0
.
.
.
I figured out that the numbers in columns 1, 4 and 7 are the atom ids in the PSF file of the last atoms in the groups defined
in the residue topology file ( toppar_drude_master_protein_2013f_mod.str). I am not sure what the numbers
0, 1 and 2 represent in the pairs of columns (2,3), (5,6) and (8,9).
Thanks in advance for the help,
Selemon
När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter. Här finns information om hur KI behandlar personuppgifter<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fki.se%2Fmedarbetare%2Fintegritetsskyddspolicy&data=02%7C01%7Cselemon%40uakron.edu%7C59e58368e78c4b8b8b1108d7ca9b286a%7Ce8575dedd7f94ecea4aa0b32991aeedd%7C0%7C0%7C637200640093393054&sdata=6a7Z7MyFMPdSwJQud26UWjPbR5LflgAkxsycX4Yf6RQ%3D&reserved=0>.
Sending email to Karolinska Institutet (KI) will result in KI processing your personal data. You can read more about KI’s processing of personal data here<https://nam03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fki.se%2Fen%2Fstaff%2Fdata-protection-policy&data=02%7C01%7Cselemon%40uakron.edu%7C59e58368e78c4b8b8b1108d7ca9b286a%7Ce8575dedd7f94ecea4aa0b32991aeedd%7C0%7C0%7C637200640093393054&sdata=%2FYpY7HGOZFkw1gyhIUSgTlY86XM0qcrvlkmVeM3%2F0MU%3D&reserved=0>.
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2020 - 23:17:13 CST