VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri May 26 2017 - 10:55:22 CDT

Hi Peter,

I have just updated the README of qwrap with an example command that should
be helpful in your case.
https://github.com/jhenin/qwrap

Jerome

On 25 May 2017 at 22:27, Giacomo Fiorin <giacomo.fiorin_at_gmail.com> wrote:

> RMSD align does more than centering, it also rotates the selection and you
> lose the alignment with the unit cell vectors.
>
> You can either subtract the COM with the Tcl command:
> set sel [atomselect top AP1]
> for { set i 0 } { $i < [molinfo top get numframes] } { incr i } {
> $sel frame $i
> $sel moveby [vecscale -1.0 [measure center $sel]]
> }
>
> or give the QWrap plugin a try:
> https://github.com/jhenin/qwrap
>
> Giacomo
>
>
> On Thu, May 25, 2017 at 10:02 PM, Peter Mawanga <
> peter.mawanga.lagos_at_gmail.com> wrote:
>
>> Thanks Giacomo, indeed, I would like to stay them at their closest
>> periodic image and the sudden jumps are a result of one of the segments
>> crossing the periodic boundary back and forth. Is there any way to wrap the
>> segments together since "fragment" hasn't been helpful?
>>
>> Unfortunately centering with "RMSD Align" didn't help either.
>>
>> On Fri, May 26, 2017 at 12:19 AM, Giacomo Fiorin <
>> giacomo.fiorin_at_gmail.com> wrote:
>>
>>> The command is working correctly, but if you are trying to make AP1 and
>>> AP2 stay at their nearest periodic image to each other, wrapping by
>>> fragment won't help, because they will be wrapped independently.
>>>
>>> You should try centering the trajectory on one of the segments (provided
>>> that it's written contiguously in the first place).
>>>
>>> Giacomo
>>>
>>>
>>> On Thu, May 25, 2017 at 3:13 AM, Peter Mawanga <
>>> peter.mawanga.lagos_at_gmail.com> wrote:
>>>
>>>> Hello to all
>>>>
>>>> I am trying to remove sudden RMSD jumps between two segments (AP1 and
>>>> AP2), observed as an artefact of periodic conditions.
>>>>
>>>> I have tried the commands below (or similar variations), but have not
>>>> been able to resolve this:
>>>>
>>>> pbc unwrap -sel "segname AP1 AP2"
>>>>
>>>> pbc wrap -all -sel "segname AP1 AP2" -compound fragment -compoundref
>>>> "segname AP1 AP2" -center unitcell -centersel "segname AP1"
>>>>
>>>> I think this should be working as per the PBCTools manual:
>>>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>>>>
>>>> Please let me know if there is any error or some omission in the
>>>> commands. Feel free to ask for further information.
>>>>
>>>> --
>>>> Cheers
>>>> Peter
>>>>
>>>
>>>
>>>
>>> --
>>> Giacomo Fiorin
>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>> Contractor, National Institutes of Health, Bethesda, MD
>>> http://goo.gl/Q3TBQU
>>> https://github.com/giacomofiorin
>>>
>>
>>
>>
>> --
>> Cheers
>> Peter
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>