VMD-L Mailing List

From: M K (mahyar.karimi20_at_gmail.com)
Date: Sat Dec 12 2015 - 03:04:10 CST

To measure the contact surface area, I use the method in this paper, which
is based on Solvent Accessible Surface Area (SASA):

K. Balamurugan, E. A. Singam, and V. Subramanian, "Effect of curvature on
the α-helix breaking tendency of carbon based nanomaterials," *The Journal
of Physical Chemistry C, *vol. 115, pp. 8886-8892, 2011.

On Sat, Dec 5, 2015 at 2:04 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Hi Bryan,
> Why not sort them so that you know that residA < residB, giving you an
> upper-triangular table array? Another thing to consider is to have a
> residlist that you reference, which saves you making atomselections inside
> the innermost loop. This is what I would do instead:
>
> set all [atomselect top "all"]
> set residlist [$all get resid]
>
> for {set i 0} {$i <= $numframes} {incr i} {
> $A frame $i
> $A update
> foreach {listA listB} [measure contacts $cutoff $A] break
> foreach indA $listA indB $listB {
> set residA [lindex $residlist $indA]
> set residB [lindex $residlist $indB]
> if { $residA > $residB } {
> set tmp $residA
> set residA $residB
> set residB $tmp
> }
> lappend contactTable($residA,$residB) $i
> }
> }
>
>
> -Josh Vermaas
>
>
> On 12/03/2015 11:05 PM, Bryan Roessler wrote:
>
>> Thanks Peter,
>>
>> I suppose then that the best way to iterate the over the list of contacts
>> then is to simply combine both atom indices lists. I had been separating
>> the atom pair lists using:
>>
>> for {set i 0} {$i <= $numframes} {incr i} {
>> $A frame $i
>> $A update
>> foreach {listA listB} [measure contacts $cutoff $A] break
>> foreach indA $listA indB $listB {
>> set selA [atomselect top index $indA]
>> set selB [atomselect top index $indB]
>> set residA [$selA get resid]
>> set residB [$selB get resid]
>> $selA delete
>> $selB delete
>> lappend contactTable($residA,$residB) $i
>> }
>> }
>>
>> but obviously that's an issue when a single resid (residA or residB) is
>> not
>> tied to either listA or listB and is randomly distributed between the two,
>> even when it is present in both *selection1* and *selection2*.
>>
>> Thus I would need to combine each list in my array by adding:
>>
>> lappend contactTable($residB,$residA) $i
>>
>> so that the contact pair is included regardless of the 'direction' of the
>> measurement.
>>
>>
>> Cheers,
>> Bryan
>>
>> *Bryan Roessler | Graduate Research Assistant*
>> UAB | The University of Alabama at Birmingham
>> *uab.edu/cmdb <http://uab.edu/cmdb>*
>> Knowledge that will change your world
>>
>> On Thu, Dec 3, 2015 at 9:14 PM, Peter Freddolino <petefred_at_umich.edu>
>> wrote:
>>
>> Hi Bryan,
>>> It isn’t really an MWE if we don’t have the structure that you’re looking
>>> at to try it out. But I’m pretty sure what you’re running into is that
>>> the
>>> elementary object being enumerated by measure contacts is the *atom pair*
>>>
>>
>