VMD-L Mailing List

From: Vikas Varshney (vv0210_at_gmail.com)
Date: Tue Oct 16 2012 - 13:37:55 CDT

Dear Axel,
Thanks, I was able to write the script and change color based on the bond
length.

Regards,
Vikas

On Tue, Oct 16, 2012 at 12:51 PM, Vikas Varshney <vv0210_at_gmail.com> wrote:

> Dear Axel,
> Thanks for the suggestions. I will try to get it working.
>
> Best Regards,
> Vikas
>
>
> On Tue, Oct 16, 2012 at 11:33 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>wrote:
>
>> On Tue, Oct 16, 2012 at 5:11 PM, Vikas Varshney <vv0210_at_gmail.com> wrote:
>> > Dear Axel,
>> > Thank you for your email and the suggestions.
>> >
>> > As you mentioned, I can load the dump file in the same molecule. That
>> should
>> > not be a problem. About the coloring scheme, I want to calculate the
>> > distance between all bonding pairs (3 pairs) for certain atom and then
>> use
>> > the largest distance among the three as the measure of the color of the
>> > atom.
>> >
>> > After reading your email, this is what I should be done. Please let me
>> know
>> > if that makes sense.
>> >
>> > 1. Read the data file using topotools
>> > 2. Retrieve the bond information (Please let me know in which variable
>> the
>> > list of lists for bonding information is stored).
>>
>> you have to choose the variable.
>>
>> set bondlist [topo getbondlist none]
>>
>>
>> https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-getbondlist-type-order-both-none-
>>
>> > Question: Is this list of lists based on the bond index (as in
>> lammps)
>> > or for each atom (as in each sub-list contains information about all of
>> its
>> > bonds)
>>
>> no, the lammps bond index is lost. VMD stores bonds in a very peculiar
>> format
>> that is optimized for fast display. you get a list where each entry has
>> the
>> atom indices that form a bond.
>>
>> > 3. If bond retrival list is like lammps (index based), Create a new
>> list of
>> > lists for each atom bond (each sublist will contain information about
>> one
>> > atom's bonding partners). Lets call this list bond3. This will be done
>> only
>> > one time.
>>
>> this information is readily available from VMD and how it stores the
>> bond information.
>> if that is what you are after, then you don't need topo getbonds, but
>> rather create
>> a selection for all atoms and then do
>>
>> set bondlist [$sel getbonds]
>>
>> in this case $bondlist will contain a list of lists with one entry per
>> atom
>> where each entry is the list of bonding partners of this atom.
>>
>> > 4. Then, for a certain frame, calculate the 3 distances for each atom
>> (using
>> > bond3 list of lists). Get the magnitude of the longest bond. Then color
>> that
>> > atom based on that distance.
>>
>> yup.
>>
>> > 5. Do this for each frame.
>> >
>> > Please let me know if you think is more appropriate. Thanks for your
>> help.
>>
>> with my proposed augmentations, that should work.
>>
>> axel.
>>
>> > Best Regards,
>> > Vikas
>> >
>> >
>> > On Mon, Oct 15, 2012 at 3:12 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> wrote:
>> >>
>> >> i am adding some comments below.
>> >>
>> >> On Mon, Oct 15, 2012 at 5:53 PM, Vikas Varshney <vv0210_at_gmail.com>
>> wrote:
>> >> > Dear John, Axel,
>> >> >
>> >> > I have a trajectory of my system of interest (CNTs) which I want to
>> >> > visualize with certain color scheme associated with retrival of bonds
>> >> > information.
>> >> >
>> >> > Basically, I am stretching a CNT and would like to color the atoms
>> based
>> >> > on
>> >> > the longest bond distance. I have looked over the forum to get some
>> >> > insights
>> >> > on how to color atoms based on user defined parameters and have the
>> >> > following TCl script which hopefully will do the job. I need some
>> help
>> >> > with
>> >> > how to retrive bond information so that I can calculated bond lengths
>> >> > for
>> >> > each atom with its bonding pairs.
>> >> >
>> >> > I am using Axel's topotools package to load the lammps data file
>> which I
>> >> > think is loading bond information as well. Below is the template of
>> the
>> >> > TCl
>> >> > script
>> >> >
>> >> > -------------------
>> >> > #/usr/bin/tclsh
>> >> >
>> >> > set lmpdata [atomselect 0 all] #This contains topology information
>> >> > set lmptrj [atomselect 1 all] #This is the trajectory file
>> >>
>> >> this looks as if you are loading the dump into a different (vmd)
>> >> "molecule".
>> >> it would be much better to load the trajectory "into" the same
>> "molecule".
>> >> if your dump contains the atom ids, the order should be preserved.
>> >>
>> >>
>> >> > for {set i 0} {$i < [molinfo 1 get numframes]} {incr i} {
>> >> > $lmptrj frame $i
>> >> > foreach atomind [$allsel get index] {
>> >> > set csel [atomselect 1 "index $atomind" frame $i]
>> >>
>> >> > # Get indices of other atoms that are connected to atom "atomind"
>> >>
>> >> this is hugely inefficient.
>> >>
>> >> since you seem to be using a conventional force field
>> >> or at least a topology file that has contains bond information,
>> >> you can do the following.
>> >>
>> >> topotools has a command to retrieve a "bond list" this is a
>> >> list of lists which contains a list of all bonds with each entry
>> >> containing the two atom indices forming the bond and additional
>> >> information, as requested. this information will not change
>> >> over the trajectory, so it can be retrieved up front and stored.
>> >>
>> >> then you should take the selection for all atoms (also defined
>> >> outside the loop) and advance it to the current frame as in your
>> >> script fragment and then retrieve all coordinate triples via
>> >> $sel get {x y z}. this will also produce a list of lists.
>> >>
>> >> now you can loop over the bond list and for each bond get
>> >> the two indices (e.g. using lassign) and then use lindex
>> >> on the coordinate list to get the two coordinate vectors and
>> >> use vecdist to compute the distance (i.e. bond length).
>> >>
>> >> now the big question is, how do you want to convert this
>> >> information into a color code, since color is stored on a
>> >> per atom basis and each atom has multiple bonding partners
>> >> (3) and you have 4 user fields to store per atom per frame
>> >> information. so theoretically it should be possible with
>> >> 3 representations using one of 3 user fields to handle
>> >> this, but you'd have to figure out a way to select the bonds
>> >> accordingly, which i currently have no idea how to do.
>> >>
>> >>
>> >> > # Calculate distance of each bond pair with one atom "atomind" using
>> >> > vector
>> >> > operators or some other functions
>> >> > # Get the largest distance (ldist)
>> >> > # Color atom
>> >> > $csel set user $ldist
>> >> > $csel delete
>> >>
>> >> creating and deleting selections during a loop and particularly
>> >> on a per atom basis, is going to be very slow, and in your
>> >> case not really needed.
>> >>
>> >> axel.
>> >>
>> >> > }
>> >> > }
>> >> >
>> >> > $lmpsdata delete
>> >> > $lmptrj delete
>> >> >
>> >> > -------------------
>> >> >
>> >> > I will highly appreciate any other suggestions as well.
>> >> >
>> >> > Best Regards,
>> >> > Vikas
>> >>
>> >>
>> >>
>> >> --
>> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> >> International Centre for Theoretical Physics, Trieste. Italy.
>> >
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>>
>
>