VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Feb 21 2013 - 06:38:45 CST

On Thu, Feb 21, 2013 at 12:30 PM, Marzieh Alishahi
<alishahi.mar_at_gmail.com> wrote:
> Dear Axel,
>
> Thank you very much for your complete explanation. Actually, I want to
> export the computed velocities and positions for all ions in each frame to
> text format, I want to perform further analysis on these results using my
> own code. Basically I have to extract positions from DCD file and velocities
> from VEL.DCD file (I used NAMD). I think it’s better to order the text files
> by serial number of atoms in order to have same id for atoms in both
> position file and velocity file. I know maybe my method is not the best, in
> fact I’m completely messed up! Do you have any idea how arranging these
> files?

this is a non-issue. atom data in VMD is *always* sorted by index
(serial is just index+1, btw) anyway. its order doesn't change over a
trajectory. neither does it change inside any dcd file.

axel.

>
> Thank you again
>
> Best,
>
>
>
> Marzieh
>
>
>
>
>
> On Thu, Feb 21, 2013 at 2:13 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Thu, Feb 21, 2013 at 10:26 AM, Marzieh Alishahi
>> <alishahi.mar_at_gmail.com> wrote:
>> > Dear VMD users
>> >
>> > I know it might be a simple question, but I will be so grateful if you
>> > help
>> > me.
>>
>>
>> > I want to put all the serial id of ion atoms in an array, I tried the
>> > following commands;
>> >
>> > set ion [atomselect top “ion”]
>> >
>> > $ion get serial
>> >
>> > The second line gives me the serial number of all atoms, which are not
>> > in
>> > array format. Can you help me how I can put this sequence of numbers in
>> > array format?
>>
>> you get a list. what do you need an array for? by what do you want to
>> index it?
>> please note that arrays in Tcl are "associative arrays" or "maps" and
>> not "vectors" or "sequential arrays" like in programming languages
>> like C, C++ or Fortran, that is that data is stored in pairs and
>> indexed via a hash table. that makes random access faster, but
>> sequential access slower than with lists. lists much more resemble
>> "sequential arrays"
>> thus lists are generally much more efficient and convenient to handle
>> when looping over its elements.
>> which is the typical case in vmd/tcl scripts. it is trivial Tcl coding
>> to convert a list into an array, e.g. via:
>>
>> set i 0
>> foreach a $list {
>> set array($i) $a
>> incr i
>> }
>>
>> please provide an example of how you want to use the data. it is
>> highly likely, that things can be done differently and more
>> efficiently.
>>
>> axel.
>>
>> axel.
>>
>> >
>> > Thanks in advance
>> >
>> >
>> > Marzieh Alishahi
>>
>>
>>
>> --
>> 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.