Hello again, fellow gmx-users,
I finally found my coding error that only set the User data for the first
half of the frames loaded, it was a simple indexing error after all.
However, I would still *greatly* appreciate any assistance with speeding up
the following loop:
for {set k 6} {$k <= 141} {incr k} {
set prot [atomselect $mol_ID "resid $k" frame $j]
set num [$prot num]
$prot frame $j
set user_list {}
set u [lindex $efield [expr $k - 6]]
for {set b 1} {$b <= $num} {incr b} {
lappend user_list $u
}
$prot set user $user_list
$prot delete
}
Is there a simpler way to accomplish the task of assigning a single User
value to individual residues without first atomselecting each one, getting
its number of atoms, and then finally looping over the atoms to build a
user_list? I'm hoping that there is some better way to do this that I
haven't thought of yet. My script runs very wonderfully except for this
chunk.
Thanks in advance for any help you can provide,
-Nathan
On Wed, May 4, 2011 at 11:06 AM, J. Nathan Scott <
scot...@chemistry.montana.edu> wrote:
> Hello all,
>
> I have written a script that does per-time-step coloring of the water
> molecules, residues, and ions in my protein based on electric field values I
> previously calculated. I received excellent help here a few months sorting
> out some problems with the script, but there is one big one remaining that I
> hope someone can help with.
>
> The problem is that only half the frames (the first half) in my simulation
> are getting colored, and I can't figure out why. This happens no matter how
> many frames I load, whether the full trajectory or just a few hundred
> frames. For what it's worth, the machine I'm running on has 12 GB of RAM, a
> very nice video card, and a new Xeon quad core processor, so I don't think
> this is an issue of system resources. At least I can see that there is still
> tons of free RAM when I am experiencing this issue.
>
> Also, I would sincerely appreciate any advice on speeding up one of my
> loops. To color the water molecules and ions I can simply atomselect them
> all, and then loop through the values from the electric field data file for
> that timestep and assign the color value to a user list either 3 or 1 times
> respectively to color each atom.
>
> However, for the residues in the protein I am having to atomselect them one
> at a time, get the number of atoms for that residue, and then do another
> loop to build a list of the correct length to assign the user values to each
> atom of the residue. Can anyone recommend a more efficient way of coloring
> the residues? When the residue coloring part of the script is stripped out
> it runs so much faster despite the fact that there are far fewer protein
> atoms than there are water or ion atoms, so I know this method of assignment
> is sluggish.
>
> Please see the script below my signature, and thank you in advance for any
> advice you can provide.
>
> --
> ----------
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University
>
>
>
>
> #######################################################################
> set first 0;
> set last 1000;
> set mut wt;
> set mut_ wt_;
> set i $first; #i will be timestep/filename indicator,
> set j 0;
>
> mol new /data/1stn/xtc/1stn_$mut.gro type gro waitfor all
> mol addfile /data/1stn/xtc/1stn_$mut.xtc type xtc waitfor all first $first
> last $l$
> set mol_ID top;
> set n [ molinfo $mol_ID get numframes ];
> animate goto 0
> animate delete beg 0 end 0 skip 0 0
> mol delrep 0 $mol_ID
>
> while {$i <= $last} {
> set fp [open "/data/1stn/$mut/pd5/pd5.stripped/1stn_$mut_$i.pd5" r]
> set file_data [read $fp]
> close $fp
>
> set data [split $file_data "\n"]
> foreach {one} $data {
> lappend efield [lindex $one 3]
> }
>
> ### Looping through residues in the for loop,
> ### selecting one residue at a time, getting its number of atoms,
> ### and then building a user value list for each of those
> ### atoms in another for loop.
>
> for {set k 6} {$k <= 141} {incr k} {
> set prot [atomselect $mol_ID "resid $k" frame $j]
> set num [$prot num]
> $prot frame $j
> set user_list {}
> set u [lindex $efield [expr $k - 6]]
> for {set b 1} {$b <= $num} {incr b} {
> lappend user_list $u
> }
> $prot set user $user_list
> $prot delete
> }
>
> ### Water loop works well
>
> set wat [atomselect $mol_ID waters frame $j]
> $wat frame $j
> set user_list {}
> for {set a 136} {$a < 10233} {incr a} {
> set u [lindex $efield $a]
> lappend user_list $u $u $u
> }
> $wat set user $user_list
> $wat delete
>
> ### Ion loop works well too
>
> set ions [atomselect $mol_ID ions frame $j]
> $ions frame $j
> set user_list {}
> for {set a 10233} {$a < 10243} {incr a} {
> set u [lindex $efield $a]
> lappend user_list $u
> }
> $ions set user $user_list
> $ions delete
>
> unset efield
> incr j 1
> incr i 2
> }
>
>
>
>
--
----------
J. Nathan Scott, Ph.D.
Postdoctoral Fellow
Department of Chemistry and Biochemistry
Montana State University
--
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