Re: AW: moving out of the box

From: Ariel Talavera Perez (
Date: Thu Feb 20 2014 - 07:48:07 CST

Hi all,

Thanks a lot for all your help. With your input I managed managed to
have the complete complex in all the frames. I first use wrap and then


On 02/17/2014 06:48 PM, MEHRAN MB wrote:
> 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,
> -Mehran
> 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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