VMD-L Mailing List

From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Sun Apr 15 2007 - 01:45:32 CDT

Thanks John, The problem was solved! I was using 1.8.5. So, updating
my VMD version is a good habit...
i will add some code t check the vmd version before running

2007/4/15, John Stone <johns_at_ks.uiuc.edu>:
>
> Hi,
> Which version of VMD are you using? There was previously
> a small memory leak in the "sidechain" selection which is fixed
> in VMD 1.8.6. If you're not using VMD 1.8.6, I would recommend
> upgrading since you're using "sidechain" in your selections and
> this may be related to the memory consumption you're observing.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Apr 15, 2007 at 01:54:48AM -0400, Guo Zhi wrote:
> > Hi all, I am trying to use a script to do statistics on sidechain
> > contact in the whole trajectory. Since the MD trajectory were yielded
> > by a home-made MD program which uses only one united atom for each
> > sidechain, the selection code might looks a little strange. Well, the
> > script seem to produce the right result, but the memory usage
> > coninuously grow up which implies certain memory leakage. I check the
> > code for several times(mainly the "atomselect" sentences) and still
> > can not find any where that cause this problem. Would anyone of you
> > bother to look into this and give me some help?
> >
> >
> > ########### Code for sidechain contact statistics ########
> >
> > set frame_no [molinfo top get numframes]
> > set res_set [lsort -increasing {"ASN" "HIS" "VAL" "THR" "LEU" "SER" "GLN"}]
> > set file_id [open "contact.dat" w]
> >
> > set sel_all [atomselect top all]
> > set res_leng [llength [lsort -unique [$sel_all get resid]]]
> >
> > for {set m 0} {$m<$frame_no} {incr m} {
> > puts $file_id "Frame $m:"
> > set all_contact {}
> > for {set i 0} {$i<$res_leng} {incr i} {
> > set tmp_sel [atomselect top "(sidechain or (not protein)) and
> > (exwithin 6.5 of ((resid $i) and (sidechain or (not protein))))" frame
> > $m]
> >
> > set contact_res [$tmp_sel get resid]
> > foreach ele $contact_res {
> > set ele_contact $i
> > lappend ele_contact $ele
> > set ele_contact [lsort -increasing $ele_contact]
> > lappend all_contact $ele_contact
> > }
> >
> > $tmp_sel delete
> > }
> >
> > set short_contact [lsort -unique $all_contact]
> > foreach ele_short $short_contact {
> > set ele_name [atomselect top "(resid $ele_short) and (name
> > CA)"]
> > set pos [lsearch -exact $short_contact $ele_short]
> > set short_contact [lreplace $short_contact $pos $pos [lsort
> > -increasing [$ele_name get resname]]]
> > $ele_name delete
> > }
> >
> > # initialize matrix
> >
> > set matrix {}
> >
> > for {set j 0} {$j<28} {incr j} {
> > lappend matrix 0
> > }
> >
> > foreach ele_short $short_contact {
> > set count 0
> > for {set j 0} {$j<7} {incr j} {
> > for {set k $j} {$k<7} {incr k} {
> > if {[lindex $ele_short 0]==[lindex $res_set
> > $j]} {
> > if {[lindex $ele_short 1]==[lindex
> > $res_set $k]} {
> > # Now set matrix element
> > set new_ele [expr [lindex
> > $matrix $count]+1]
> > set matrix [lreplace $matrix
> > $count $count $new_ele]
> > }
> > }
> > incr count
> > }
> > }
> > }
> >
> > puts $file_id $matrix
> > }
> >
> > $sel_all delete
> > close $file_id
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
Guo Zhi