From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 06 2012 - 01:01:41 CST
The periodic cell in NAMD is set by cellbasisvector. PMEgridsize is the grid size for the "particle mesh ewald" long range electrostatics and should be set as explained in the manual, whereas the cellbasisvectors should set right to your cell size. For such a system I would lay the membrane as X,Y and then let pressure happen in Z with useconstantarea. Why? Because you don't want your membrane to get squeezed, only to compress your solvent a little, right? Even if you have such experimental constant dimensions to keep.
Feel free to ask.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von R. Charbel Maroun
> Gesendet: Freitag, 3. Februar 2012 15:54
> An: Ajasja Ljubetič
> Cc: Norman Geist; Boyang Wang; Namd Mailing List
> Betreff: Re: AW: namd-l: Energy minimization of membrane
> No, I haven't run the equilibration in CHARMM 'cause I'm using NAMD.
> In C-GUI's step5_assembly.str, I see :
> SET BOXTYPE = RECT
> SET XTLTYPE = TETRAGONAL
> SET A = 85.3711
> SET B = 85.3711
> SET C = 108.095
> SET ALPHA = 90.0
> SET BETA = 90.0
> SET GAMMA = 90.0
> SET ZCEN = 0.0
> SET NLIPTOP = 94
> SET NLIPBOT = 94
> SET NWATER = 15800
> SET NPWATER = 3
> SET POSID = POT
> SET NEGID = CLA
> SET NPOS = 45
> SET NNEG = 45
> So, no problem for A, B, C. Is ZCEN the cellOrigin? If I don't use
> Charmm, where do I get the grid size ? I found the following in the
> namd wiki :
> "The PME grid size should be about one cell per Angstrom in each
> dimension, with factors of 2, 3, and 5 to be sure that the FFT is
> efficient (i.e., order N log N complexity). Newer versions of NAMD
> will pick this automatically if you set "pmeGridSpacing 1.0", but the
> grid may change when a constant pressure simulation is restarted." So,
> something like 90, 90 and 111 should be suitable.
> On another hand, using
> useFlexibleCell yes
> useConstantRatio yes
> I'm afraid that the cell will get distorted and not respect anymore
> the starting experimental cross-sectional area (63A² for DPPC).
> Wouldn't it be better to use useConstant Area ?
> Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com> a écrit :
> > Hi,
> >> I used CHARMM-GUI for building my membrane system.
> > Did you run the equlibration in CHARMM as well? If so, just open the
> > file step6.6_equilibration.str, where you have the box size (A, B, C)
> > the FFT grid size information.
> > If you didn't run the equilibration in charm then look
> > into step5_assembly.str.
> > Usually I ignore the grid used by charmm and just set PMEGridSpacing
> to 1.0.
> > You might also want to use
> > useFlexibleCell yes
> > useConstantRatio yes
> > Best regards,
> > Ajasja
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