VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Nov 06 2017 - 15:49:48 CST

Err... I see I screwed up. The 800 length guys are just a variation on the 2-away ones (which shouldn't have a "not" in the withinbonds 2 selection). In general, your neighbor selection would be something like:
set neighborsel [atomselect top "index $endidx or ((not withinbonds $n of index $endidx) and (withinbonds [expr {$n+1}] of index $endidx))"]
-Josh

This works so long as your polymer is linear. :)

On 11/06/2017 02:46 PM, Clement Fang Jin Koh wrote:
Ah I see! This would work! The only downside I see for this is that the conditions for the selections can get out of hand fast for really long chains, and I have chains as long as 800 beads.

But thank you! This was helpful!

-Clement

On Mon, Nov 6, 2017 at 4:12 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
AHAH!!! Well this is much easier then, since it is symmetric, and you only care about the distance between stuff, so the order doesn't matter. First, you'd find your ends:

set endsel [atomselect top "numbonds == 1"]

Then you'd get the corresponding index for each of the ends. If you wanted the neighbor, you'd do something like:

foreach endidx [$endsel get index] {
    set neighborsel [atomselect top "withinbonds 1 of index $endidx"]
    #This is now a pair of atoms that are adjacent to one another
    puts [$neighborsel get index]
}

For those that are 2-away from the end, you would do something like:

foreach endidx [$endsel get index] {
    set neighborsel [atomselect top "index $endidx or ((not withinbonds 1 of index $endidx) and (not withinbonds 2 of index $endidx))"]
    #This is now a pair of atoms that are adjacent to one another
    puts [$neighborsel get index]
}

You can play similar games if you want internal distances, but I'll let you work those out yourself.

-Josh

On 11/06/2017 01:58 PM, Clement Fang Jin Koh wrote:
Hi Josh,

My polymers are polymers with coarse-grained beads with LJ potentials and each of my systems have different polymer chain lengths. My initial configuration had each polymer chain with indices in running order, so {0 1 2 3 4 5} were bonded together and {6 7 8 9 10 11} were bonded together and so on and so forth. Due to a bond swapping algorithm in LAMMPS, the indices ended up being messed up but the chain lengths are preserved, where after the bond swapping, the chains could become {11 1 2 3 4 5} {6 7 8 9 10 0}. I am trying to find the internal end to end distances for each chain, thus I would need to refer to the "right" index along the chain. Hope this makes sense.

Best,
Clement

On Mon, Nov 6, 2017 at 3:42 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>> wrote:
Hi Clement,

Do you mind me asking what the polymer is? I'm having a hard time conceptualizing a polymer with only 6 atoms in it, especially one whose order changes depending on the fragment. If you were dealing with a linear polymer, you could pick the end of a polymer with something like "numbonds == 1", except that will give you *both* ends of a linear polymer. Or, if the offsets are consistent, you can rearrange the list yourself in Tcl. For instance, to rearrange your output index list, you could do something like:

set idxlist [list 1 2 3 4 5 6]
set orderlist [list 3 5 4 2 1 0]
set newlist [list ]
foreach order $orderlist {
lappend newlist [lindex $idxlist $order]
}
puts $newlist

Do either of those make sense for your polymer topology?

-Josh

On 11/06/2017 12:58 PM, Clement Fang Jin Koh wrote:
Hi Josh,

The only way I can tell in VMD is by looking visually at the OpenGL display window. If it helps, I loaded a lammpsdata file for my system into VMD. It seems like I only can get a list of all the indices in each chain by getting "fragment #". Their resids are different in the sense that for a chain of 6 atoms, they are numbered {3 2 1 1 2 3}. Selecting their resids as well as the fragment might help but I need to be able to sequentially go down the chain (select atom #1 and atom #2, atom #1 and atom #3 and so on). I would be really grateful if you have any suggestions.

Best,
Clement

On Mon, Nov 6, 2017 at 12:39 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>><mailto:Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov><mailto:Joshua.Vermaas_at_nrel.gov<mailto:Joshua.Vermaas_at_nrel.gov>>>> wrote:
Hi Clement,

No. VMD will always return indicies in order because of how the return
list is assembled. Normally, the way to get around this it to make a
selection that WILL give you what you want. How can you tell which atoms
are "first" or "second"? Do they have specific names? Are their resids
different somehow? Is it based on bonding?

-Josh

On 11/05/2017 10:37 PM, Clement Fang Jin Koh wrote:
> Hi,
>
> I have a system of polymer chains, whose atom indexes of each chain
> are not in sequential order (i.e. instead of {1 2 3 4 5 6}, they could
> be {4 6 5 3 2 1}). For my tcl analysis script I need to reference the
> first and second atoms on each chain, then the first and third, and so
> on.
>
> I tried doing so by atomselecting the fragment, then getting the
> indexes. But vmd seems to rearrange the index list to be in sequential
> order. So {4 6 5 3 2 1} becomes {1 2 3 4 5 6}. So I am unable to
> reference the correct atom on the chain by lindex of the index list.
>
> Is there another way to reference the chain atoms? Or another way to
> get the indexes without having them pre-sorted?
>
> Thanks,
> Clement