Re: NAMDEnergy Plugin - setting PMEGridSize / mesh density

From: Michael S. Sellers (Cont, ARL/WMRD) (michael.s.sellers.ctr_at_us.army.mil)
Date: Wed May 11 2011 - 15:29:25 CDT

Lela,

According to namdenergy.tcl, the plugin sets PMEGridSize equal to
1.2*(Max-Min) of your system. I would make sure what you have loaded
into VMD is accurately represented by your .xsc file, and that you have
correctly filled in the Selection boxes.

-Mike

..
set notsel [atomselect $currentMol all frame first]
set oldbetas [$notsel get beta]
set xyz [vecsub [lindex [measure minmax $notsel ] 1] [lindex [measure
minmax $notsel] 0]]
..
..
..
if {$extsystem != ""} {
   puts $namdconf "extendedSystem\t\t\t $extsystem"
   lappend remjob_inputfiles "$extsystem"
   if {$pme != 0} {
     puts $namdconf "PME on\nPMEGridSizeX [expr int([lindex $xyz 0] *
1.2)]\nPMEGridSizeY [expr int([lindex $xyz 1] * 1.2)]\nPMEGridSizeZ
[expr int([lindex $xyz 2] * 1.2)]\n"
   }
 }

Lela Vukovic wrote:
> Hello,
>
> I have a question about the NAMDEnergy Plugin: has anybody found a way
> to set the PMEGridSize when running this plugin, rather than it being
> automatically specified (as stated at:
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/ )?
>
> We have an error of incompatible cell size (xsc file) with the
> PMEGridSize: 256 A (set by us) versus 133 A (chosen automatically),
> which gives us the following error:
>
> FATAL ERROR: PMEGridSizeX 133 is too small for cell length 256.000000
> and PMEGridSpacing 1.500000
>
> Thank you,
> Lela
>
>


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