Re: Fwd: Fwd: hi

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jun 02 2011 - 12:52:25 CDT

please do everybody a favor and write a "proper" message
with a suitable subject line and recognizable content,
instead of forwarding the forward of a forwarded mail.
it is near impossible to tell what you are asking.

your chances to have somebody even read, let alone reply
with something useful to you, are getting smaller with
each forward.

thanks in advance,
      axel.

On Thu, Jun 2, 2011 at 1:44 PM, kanchi subbarao rao <ksubbu85_at_gmail.com> wrote:
>
>
> ---------- Forwarded message ----------
> From: kanchi subbarao rao <ksubbu85_at_gmail.com>
> Date: Thu, Jun 2, 2011 at 12:02 AM
> Subject: Fwd: Fwd: hi
> To: namd-l_at_ks.uiuc.edu
>
>
>
>
> ---------- Forwarded message ----------
> From: kanchi subbarao rao <ksubbu85_at_gmail.com>
> Date: Wed, Jun 1, 2011 at 9:51 PM
> Subject: Fwd: Fwd: hi
> To: fzhu_at_wag.caltech.edu
>
>
>
>
> ---------- Forwarded message ----------
> From: kanchi subbarao rao <ksubbu85_at_gmail.com>
> Date: Wed, Jun 1, 2011 at 10:36 AM
> Subject: Re: Fwd: hi
> To: Fangqiang Zhu <fzhu_at_wag.caltech.edu>
>
>
> thank you Fangqiang Zhu
> it is now working. but i have a doubt "in vmd also we always call the psfgen
> while creating a psf and pdb files.it is working then with out namd.   what
> is the difference between that and this ?
> what changes i have to do in make_arm.tcl  to create graphene-sheet instead
> of nano tubue?
> shall you sagest me ?
>
>
>
>
>
>
> thanks
> subbarao kanchi.
>
>
> On Tue, May 31, 2011 at 7:11 PM, Fangqiang Zhu <fzhu_at_wag.caltech.edu> wrote:
>>
>> To use this script you need to install psfgen first, which usually
>> comes with the NAMD binary...
>>
>> On Tue, 31 May 2011, kanchi subbarao rao wrote:
>>
>> > ---------- Forwarded message ----------
>> > From: kanchi subbarao rao <ksubbu85_at_gmail.com>
>> > Date: Tue, May 31, 2011 at 11:24 AM
>> > Subject: Fwd: hi
>> > To: jordi_at_ks.uiuc.edu
>> >
>> >
>> >
>> >
>> > ---------- Forwarded message ----------
>> > From: kanchi subbarao rao <ksubbu85_at_gmail.com>
>> > Date: Tue, May 31, 2011 at 11:23 AM
>> > Subject: hi
>> > To: jordi_at_ks.uiuc.edu
>> >
>> >
>> > hi ,
>> >
>> >             i am doing nanotubes tutorial, in that  to build the nano
>> > tubes
>> > there is given a make_arm.tcl file.
>> > that is given below
>> >
>> >
>> > # Written by Fangqiang Zhu, 6/3/2002
>> >
>> > # Make a m*m nanotube with length n.
>> > # Write to $output.psf and $output.pdb
>> >
>> >
>> > proc make_arm {m n output} {
>> >
>> >   # Bond length
>> >   set a 1.3750
>> >   set PI 3.141592654
>> >   set tt [expr 2*$PI/(3*$m)]
>> >   set r [expr $a/(2*sin($PI/3/$m))]
>> >
>> >   set fd_top [open temp_armchair.top w]
>> >   # Version number
>> >   puts $fd_top "0 0"
>> >   puts $fd_top "MASS     1 CA    12.01100 C"
>> >   puts $fd_top "AUTO ANGLES DIHE"
>> >   puts $fd_top "RESI ARM          0.00"
>> >
>> >   set fd_pgn [open temp_armchair.pgn w]
>> >   puts $fd_pgn "topology temp_armchair.top"
>> >   puts $fd_pgn "segment NT {residue 1 ARM}"
>> >
>> >   # Define the atom names for each carbon
>> >   set ind 0
>> >   for {set i 0} {$i<$n} {incr i} {
>> >     for {set j 0} {$j<$m} {incr j} {
>> >       for {set k 0} {$k<2} {incr k} {
>> >         if {$ind > 99} {
>> >           set name($i,$j,$k) C$ind
>> >         } elseif {$ind > 9} {
>> >           set name($i,$j,$k) C0$ind
>> >         } else {
>> >           set name($i,$j,$k) C00$ind
>> >         }
>> >         incr ind
>> >       }
>> >     }
>> >   }
>> >
>> >   for {set i 0} {$i<$n} {incr i} {
>> >     set z [expr ($i-($n-1)/2.0)*sqrt(3)/2*$a]
>> >     set t0 [expr ($i%2==0)?0:1.5*$tt]
>> >     for {set j 0} {$j<$m} {incr j} {
>> >       puts $fd_top "ATOM $name($i,$j,0) CA      0.00"
>> >       set t [expr $t0+(3*$j-0.5)*$tt]
>> >       puts $fd_pgn "coord NT 1 $name($i,$j,0) {[expr $r*cos($t)] [expr
>> > $r*sin($t)] $z}"
>> >       puts $fd_top "ATOM $name($i,$j,1) CA      0.00"
>> >       set t [expr $t0+(3*$j+0.5)*$tt]
>> >       puts $fd_pgn "coord NT 1 $name($i,$j,1) {[expr $r*cos($t)] [expr
>> > $r*sin($t)] $z}"
>> >       puts $fd_top "BOND $name($i,$j,0) $name($i,$j,1)"
>> >       if {$i%2 == 1} {
>> >         set ii [expr $i-1]
>> >         set jj [expr ($j+1)%$m]
>> >         puts $fd_top "BOND $name($ii,$j,1) $name($i,$j,0)"
>> >         puts $fd_top "BOND $name($ii,$jj,0) $name($i,$j,1)"
>> >       } elseif {$i > 0} {
>> >         set ii [expr $i-1]
>> >         set jj [expr ($j-1)%$m]
>> >         puts $fd_top "BOND $name($ii,$jj,1) $name($i,$j,0)"
>> >         puts $fd_top "BOND $name($ii,$j,0) $name($i,$j,1)"
>> >       }
>> >     }
>> >   }
>> >
>> >   puts $fd_pgn "writepsf $output.psf"
>> >   puts $fd_pgn "writepdb $output.pdb"
>> >
>> >   close $fd_top
>> >   close $fd_pgn
>> >
>> >   exec psfgen temp_armchair.pgn
>> >   exec rm temp_armchair.top
>> >   exec rm temp_armchair.pgn
>> > }
>> >
>> >
>> > while building nano tube in tcl-console by  the commands
>> > *make arm 6 12 nanotube*
>> > *
>> > *
>> > i am getting the error *couldn't execute "psfgen": no such file or
>> > directory *
>> > i can not debug this error shall you helpme?
>> >
>> >
>> >
>> >
>> > thanking you
>> > subbarao kanchi.
>> >
>>
>
>
>
>
>

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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