VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 10 2010 - 17:41:03 CST

On Wed, Mar 10, 2010 at 5:27 PM, Florentina Tofoleanu
<florentina.tofoleanu_at_gmail.com> wrote:
> Hello,

hi florentina,

[...]

> $refA update

this update is not really needed. this selection will not change.

> $refB update
>
> set nhb [llength [lindex [measure hbonds 3.1 60 $refA $refB] 0]]

here is the culprit. while $refB will select positions with PBC in mind,
it actually does not include multiple copies of the coordinates and thus
measure hbonds will only compute the distances to the original
coordinates of all particles. i.e. it is not PBC aware and thus you
get in both cases the same result.

if you cell is large enough, you might want to try running
pbc wrap with providing $refA (or rather its center of mass)
as the reference point for the center of the wrapping.
this way your "within" selection should be ok.

>
> puts $outfile "$frame $nhb"
>
> }
>
> close $outfile
>
>
> Is there an error in the script, or just the pbwithin command won't do?
>
> I've seen in this post
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14664.html
> "(Pbwithin) does not, however, modify the coordinates - they will still be
> the coordinates of the atom in the primary  image, so if you want to compute
> distances, you need to take into account the periodic boundary conditions
> manually. " Could Olaf, or anybody else, explain what taking into account
> the pbc manually mean and how can I change my script?

how about adding?

pbc wrap -molid $mol -compound res -centersel $refA -first $frame -last $frame

(add -orthorhombic for more speed, if your cell is orthorhombic)

cheers,
    axel.

>
> Thank you,
>
> Florentina
>
>
> On Sat, Sep 19, 2009 at 9:55 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> 2009/9/19 Thomas Evangelidis <te8624_at_mbg.duth.gr>:
>> > Hi Katherine,
>> >
>> > lets say you want to count all the waters(TIP3) within 5 A of resids
>> > 1-50
>> > taking into account waters in the nearest periodic cells, then the
>> > command
>> > should be:
>> >
>> > llength [[atomselect top "(oxygen pbwithin 5 of (protein and resid 1 to
>> > 50))
>> > and resname TIP3"] list]
>>
>> folks,
>>
>> when giving code examples, please make sure that you give examples
>> of _good_ coding. this piece of code has a high risk of creating a memory
>> leak
>> and is inefficient.
>>
>> the same can be done by:
>>
>> set sel [atomselect top "(oxygen pbwithin 5 of (protein and resid 1 to
>> 50)) and resname TIP3"]
>> puts "found [$sel num] water molecules"
>> $sel delete
>>
>> and this code uses the "num" option to do the counting in c rather
>> than creating a tcl
>> list and counting its length and show that the functions created by
>> atomselect have to
>> be deleted after use (it is better to always manually delete them
>> rather than counting
>> on tcl to clean up).
>>
>> > I have an alpha version of a plugin to truncate trajectories and keep
>> > only a
>> > specified number of waters within R Angstroms of an atomselection, it
>> > might
>> > be helpful to your analysis.
>>
>> that reminds me. having you been able to sort out your issues with bigdcd?
>> did the improved re-rentrant version of bigdcd work for you?
>>
>>
>> thanks,
>>    axel.
>> >
>> > regards,
>> > Tom
>> >
>> >
>> >> Dear VMD users:
>> >> My sytem contains 18 proteins in a unit cell.  I also have several 20ns
>> >> trajectories (*.dcd) of this system.
>> >> I would like to calculate the distribution of the water molecules
>> >> around
>> >> each one of the proteins and around the different amoinoacids that
>> >> compose
>> >> them during the trajectories.
>> >> I've been trying to find another VMD mail list posted message
>> >> containing
>> >> this question and somewhere in the VMD user's guide but I haven't found
>> >> anything related.
>> >> I've worked with some scripts in VMD, using the atomselect command and
>> >> doing
>> >> loops along trajectories.
>> >> What I need is some help with the right command to count water
>> >> molecules
>> >> (TIP3) around a specific part of the protein.
>> >> Thank you in advance.
>> >> KP
>> >>
>> >
>> >
>> > ----- End message from kparra_at_mail.usf.edu -----
>> >
>> >
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
>> Institute for Computational Molecular Science
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Florentina Tofoleanu
> Postgraduate Research Fellow
> Theoretical and Computational Biophysics Group
> University College Dublin
> School of Physics, Rm. 110
> Belfield, Dublin 4, Ireland
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.