Re: AW: moving out of the box

Date: Mon Feb 17 2014 - 11:48:44 CST

Hi Ariel,

yeah, I have seen that a lot. There are few way to fix the representation
based on the complex situation.

1- if the complex segments move almost together and they are mostly close
to each other; then, you just need to use RMSD trajectory tool in VMD, as
Aron mentioned, and align the complex with its first frame in which all
segments were in the middle of water box. In this way, there is no need to
use unwrap command at all.

2- if they do not move together, for instance, some segments stay in the
middle of the box while the others are searching near the box boundary,
then you need to use 'wrap' or 'unwrap' command. firstly I need to make
sure by saying 'not restrain the neither the translation nor the rotation
of the complex' you meant that you have not used 'wrapall on' in your NAMD
Config or not. Since it is not constrain and it is just the way of
representing. Therefore:

2-a, if you already used 'wrapall on' command in NAMD config file, it also
moves your monomer to the other side of your box when it passes the
boundary. In this case, you need to use what Norman said but 'unwrap'
instead of 'wrap'
pbc unwrap -all -compound res -center com -centersel "protein or nucleic"
then you could use RMSD trajectory tool in VMD to align the complex with
first frame.

2-b, if you have not used 'wrapall' in NAMd config or it is off,then you
need to used exacly what Norman mentioned before,
pbc wrap -all -compound res -center com -centersel "protein or nucleic"
then you could use RMSD trajectory tool in VMD to align the complex with
first frame

in worst case scenario, it has happened to me few times, above solutions do
not work, and I would construct neighbour cell by loading complex and
moving all frames by the box length and then record what I am interested in.

Hope it works for you,


On Mon, Feb 17, 2014 at 5:39 AM, Ariel Talavera Perez <>wrote:

> Yes Kenno, the bonds seems cross the whole after the wrapping.
> Aron, I followed your suggestion but it seems to increase the problem.
> One more question. Is always possible to solve that wrapping problem?
> Thanks again
> Ariel
> On 02/14/2014 08:25 PM, Aron Broom wrote:
>> pbc wrap -centersel "protein or nucleic" -center com -compound residue
>> -all

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