From: R. Charbel Maroun (charbel.maroun_at_inserm.fr)
Date: Fri Feb 03 2012 - 08:53:37 CST
Hi,
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 ?
Cheers,
CM
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) and
> 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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