Re: AW: Energy minimization of membrane

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Feb 09 2012 - 01:25:56 CST

To get the basis vectors, you can load your system in VMD and open
Extensions > Tk Console. In the console enter the below function or
else save it in a text file and from the console type: source
directoryToYourTextFile/nameOfYourTextFile.

proc get_cell {{molid top}} {
  set all [atomselect $molid all]
  set minmax [measure minmax $all]
  set vec [vecsub [lindex $minmax 1] [lindex $minmax 0]]
  puts "cellBasisVector1 [lindex $vec 0] 0 0"
  puts "cellBasisVector2 0 [lindex $vec 1] 0"
  puts "cellBasisVector3 0 0 [lindex $vec 2]"
  set center [measure center $all]
  puts "cellOrigin $center"
  $all delete
}

Now make sure your molecule is the top molecule in VMD (ie has the T
in it's line in the "VMD Main" window). Then in the console type:
get_cell. The basis vectors for your system should be output.

To determine the optimal PME Grid spacing, either use PMEGridSpacing
1.0, as previously suggested or for each cartesian axis find a factor
of 2, 3, 5, etc that when divided by the corresponding axis' basis
vector yields a result as close to 1.0 as possible.

Best,
Chris

On Fri, Feb 3, 2012 at 8:53 AM, R. Charbel Maroun
<charbel.maroun_at_inserm.fr> wrote:
> 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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>
>

-- 
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 773-570-6078
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078

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