VMD-L Mailing List

From: Vishal Kopardé (vishal.koparde_at_alumni.vanderbilt.edu)
Date: Fri Oct 19 2007 - 09:03:24 CDT

Hello,
   I am having a very weird problem with bigdcd, that the number of
frames accessed is equal to the number of new line characters following
the bigdcd statement. How do I get over it? I have 5000 frames in my dcd
file and right now I am adding 5000 blank lines after the bigdcd
statement in the tcl file.
    This problem was reported earlier but I could not find a
straightforward solution.

tcl script
**********************
source bigdcd.tcl

proc zeros {num} {
set list1 {}
for {set i 0} {$i<$num} {incr i} {
lappend list1 0
}
return $list1
}

proc sumlists {list1 list2} {
if {[llength $list1] != [llength $list2] } {
echo " ERROR lists are unequal "
return
}
set list3 {}
foreach i $list1 j $list2 {
lappend list3 [expr $i + $j]
}
return $list3
}

set psffile hex.psf
set dcdfile prod1.dcd
set hblength 3.50
set rshell 4.0
set hbangle 30

set res {}
for {set k 1} {$k <=21} {incr k} {
    lappend res $k
    set f2 [open ${k}pmol1.dat w]
    close $f2
    unset f2
    set f2 [open ${k}pmol2.dat w]
    close $f2
    unset f2
    set f2 [open ${k}pmol1num.dat w]
    close $f2
    unset f2
    set f2 [open ${k}pmol2num.dat w]
    close $f2
    unset f2
}
set res1 {}
for {set j 1} {$j <=30} {incr j} {
    set k [expr $j+21]
    lappend res1 $j
    set f2 [open ${k}pmol1.dat w]
    close $f2
    unset f2
    set f2 [open ${k}pmol2.dat w]
    close $f2
    unset f2
    set f2 [open ${k}pmol1num.dat w]
    close $f2
    unset f2
    set f2 [open ${k}pmol2num.dat w]
    close $f2
    unset f2
}
   
proc doit { i } {
    global res res1 hblength hbangle rshell
**********
 STATEMENTS
************
}

    mol delete all
    mol load psf $psffile
    bigdcd doit $dcdfile

5000 blank lines here
************

   Your help is greatly appreciated.
Thank you,
Vishal 

-- 
Vishal N Kopardé, Ph.D.
http://www.people.vcu.edu/~vnkoparde/