From: Vermaas, Joshua (
Date: Tue Aug 09 2016 - 11:42:07 CDT

Hi Stepahnie,

Fragment 1 will still jump unless you align it afterwards, since fragment 1 will naturally diffuse around the system. If you want a fixed reference point, you'll need to align everything afterward. If you want a diffusing reference point, the better way to do it would be to say something like:

pbc unwrap -all -sel "protein"
pbc wrap -compound fragment -center com -centersel "protein"

This is the alternative way of solving the jumping protein problem, but I found it slower, and would align my trajectories afterward anyway.

On 08/09/2016 09:30 AM, kim, stephanie S. wrote:

Hi Josh,

Thank you for the tip. But I'm still having the same problem even after adding -all command at the end. After using "pbc wrap -compound fragment -center com -centersel "fragment 1" -all", fragment 1 still jumps around.

I know you have mentioned that for most multimers pbc wrap will put the other elements in the same box, but is there any other suggestions to fix this problem?

Thank you,

Stephanie Kim

From: Vermaas, Joshua <><>
Sent: Thursday, August 4, 2016 12:06:56 PM
To: kim, stephanie S.;<>
Subject: Re: vmd-l: Aligning a dcd file of a protein consisting two chains

Ahh, I forgot the -all, which is why it only did it for the last frame, which might have already been correct so you didn't notice. This procedure will not change the coordinates stored in your dcd unless you instruct VMD to write a new dcd with the repositioned atoms (with something like animate write dcd rewrapped.dcd, look up the exact syntax in the userguide).


On 08/04/2016 08:02 AM, kim, stephanie S. wrote:

Hi Joshua,

I've tried your suggestions, and after typing them in it said:

Info) 100.0% complete (frame 49999)

But nothing happened to my trajectory.

I've loaded the psf and dcd file and opened the TkConsole to type in pbc wrap commands. Am I doing this wrong?

If I do pbc wrap commands, will it overwrite the existing dcd file?

Thank you,


From: Vermaas, Joshua <><><><>
Sent: Wednesday, August 3, 2016 2:24:32 PM
To: kim, stephanie S.;<><>
Subject: Re: vmd-l: Aligning a dcd file of a protein consisting two chains

Hi Stephanie,

The way I like doing it is through two successive calls to pbctools.

pbc wrap -compound fragment -center com -centersel "chain A"

pbc wrap -compound fragment -center com -centersel "protein"

The idea behind these two commands is that the first will center is on one component of the protein. For most multimers, that will also put the other elements in the same box, and so you eliminate jumps that way. The second line then recenters it so that the protein as a whole is in the center of the box, not just one fragment. The second one could be replaced by another alignment script if you prefer.

-Josh Vermaas

On 08/03/2016 11:31 AM, kim, stephanie S. wrote:


I've tried to align a trajectory of a protein consisting two chains, but when I load the aligned version of the trajectory, two chains separate, jump around for couple of frames and then would come back. A colleague suggested using ptraj commands: "center" and "image center familiar" instead, because he had the same problem before with aligning a trajectory consisting two subunits using vmd.

Can you suggest any other tcl scripts that would fix this problem? Or could you suggest a script that correlates to the ptraj command "center" and "image center familiar"?

I've used this script to align the trajectory:


proc align { rmolid smolid2 seltext } {
  set ref [atomselect $rmolid $seltext frame 0]
  set sel [atomselect $smolid2 $seltext]
  set all [atomselect $smolid2 all]
  set n [molinfo $smolid2 get numframes]

  for { set i 1 } { $i < $n } { incr i } {
    $sel frame $i
    $all frame $i
    $all move [measure fit $sel $ref]
$ref delete
$all delete
$sel delete

align 0 0 "protein"


Thank you,

Stephanie Kim

Graduate Student

Department of Chemistry and Biochemistry

The Ohio State University

2116 Newman & Wolfrom Laboratory

100 W. 18th Ave
Columbus, OH 43210