From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Thu Sep 27 2018 - 18:07:09 CDT
Although Brian is correct in his statement regarding NAMD's handling of water molecules, his answer actually does not address the question.
The answer is that the second column is not a list of atom indices. Rather it is a list that indexes the array of integers that follows the parameters section of NUMLP.
For the entries in the NUMLP section (I'll restate the lines here):
3 1 F -0.240345 0.00000 0.00000
3 5 F -0.240345 0.00000 0.00000
3 9 F -0.240345 0.00000 0.00000
3 13 F -0.240345 0.00000 0.00000
the 3 in the first column means that the lone pair has 3 support atoms, and the 1, 5, 9, 13, in the section column refers to the index list that follows this force parameters list. For the index list that follows, position 1 is the index of the first lone pair with indices for its 3 supporting atoms, then position 5 is the index of the second lone pair with indices for its 3 supporting atoms, etc. The 3 real numbers for each entry in NUMLP provide the parameters needed for repositioning a lone pair with respect to its support atoms.
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Sep 27, 2018, at 8:41 AM, Brian Radak <brian.radak_at_gmail.com> wrote: > > Hi Julian, > > Without looking back at the code, I don't have an answer which speaks directly to your inquiry. However, I will say that all water models in NAMD (including lone pair models) have specialized routines that often ignore some or all of the LPHOST section of the PSF. Thus, while I suspect there is a logical explanation for that format, it's also possible that it will not exactly match the NAMD internals,which instead use heuristics based on atom masses, etc. > > HTH, > BKR > > On Thu, Sep 27, 2018, 3:49 AM Julian Müller <mueller_at_pctc.uni-kiel.de <mailto:mueller_at_pctc.uni-kiel.de>> wrote: > Hello, > > i am trying to set up different solvent boxes using the drude > polarizable SWM4-NDP water model. I downloaded the example files for 216 > SWM4-NDP water from https://www.ks.uiuc.edu/Research/Drude <https://www.ks.uiuc.edu/Research/Drude>. I am a > little puzzled by the !NUMLP NUMLPH section, especially the exact > meaning of the second entry in the following lines: > > 3 1 F -0.240345 0.00000 0.00000 > 3 5 F -0.240345 0.00000 0.00000 > 3 9 F -0.240345 0.00000 0.00000 > 3 13 F -0.240345 0.00000 0.00000 > > Searching available documentation it seems this number identifies the > host atom the lone pair is attached to. Therefore i would intuitively > expect the numbers to be 1, 6, 11 (i.e. the atom IDs of the Oxygen > atoms) and ascending from there up to the total number of atoms in the > system, since the number of atoms per SWM4-NDP water is 5 including the > drude particle. Is there a reason that this number is incremented by 4 > per lone pair and not by 5? Am i interpreting the line incorrectly or is > there maybe an error with this .psf file due to the conversion from a > four atom TIP4P model? Any help here would be greatly appreciated. > > best regards > > Julian Müller > > -- > Dr. Julian Müller > Institute for Physical Chemistry > Christian-Albrechts-Universität zu Kiel > Max-Eyth Strasse 2 > 24118 Kiel > > phone: 0049 431 880-5820 > e-mail: mueller_at_pctc.uni-kiel.de <mailto:mueller_at_pctc.uni-kiel.de> >
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