4
$\begingroup$

I am doing a simulation of multiple polymers which are named with segnames U(integer). During the course of simulation two polymers U5 and U10 interact with each other. However, because of periodic boundary conditions when I measure the accessible area or radius of gyration I get unnaturally large values.

I have tried to wrap periodic boundaries by running the command

pbc wrap -all -centersel "segname U5 U10"

My reasoning is I want the U5 U10 aggregate at the center of the simulation box. However, this causes the polymer to fragment and again does not give proper result. Can you suggest proper pbc wrap arguments for this situtation?

$\endgroup$

1 Answer 1

4
$\begingroup$

If you need to wrap a simulation trajectory using VMD, and want to ensure that the molecules remain as is (and no artifacts are introduced) use the following command:

pbc wrap -all -centersel "selection" -center com -compound residue

Here the -compund residue flag instructs VMD to wrap the trajectory in such a way that atoms of one residue id does not get broken while wrapping is performed.

$\endgroup$
2
  • $\begingroup$ using selection as segname U5 did what I required. $\endgroup$
    – Roni Saiba
    May 11, 2023 at 4:09
  • 1
    $\begingroup$ minor correction to the command -> centersel should be -centersel. $\endgroup$
    – Roni Saiba
    May 12, 2023 at 4:41

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .