From: Nicolas Martin (
Date: Fri Feb 19 2016 - 12:14:44 CST

I don't know how to check if the pbc box is defined. Although when I
draw it using pbc box command in the Tkconsol I can see that it is not
fully overlapping my current "atom box". Only one forth is overlapping
the box drawn by PBCtools.


On 02/19/2016 07:10 PM, Josh Vermaas wrote:
> Ok. Next troubleshooting element: is the pbc box defined? This
> combination has worked for me in the past, so I'm a bit confused as to
> why it isn't working here. :(
> -Josh
> On 02/19/2016 12:04 PM, Nicolas Martin wrote:
>> Dear Josh,
>> According to the documentation of PBC tools, sel is what will be
>> wrapped and centersel what is used to center the box. Here I want to
>> wrap the protein and center the segment A, uppon the command you
>> adviced me to use.
>> I double checked just to make sure and in the case of my system chain
>> A contains the same atoms as segment A. And thus should be centered
>> in the box.
>> Nick
>> On 02/19/2016 06:54 PM, Josh Vermaas wrote:
>>> If you want it centerd in the box, drop the -sel "protein" at the
>>> end. I was just trying to get the protein together into one unit
>>> cell, so that you can move them as a unit later. Next question: is
>>> the segname really A, or is it chain A, B, C, D, and E? VMD's
>>> atomselections matter! If segname A is an empty selection, it won't
>>> do what you want.
>>> -Josh
>>> On 02/19/2016 11:48 AM, Nicolas Martin wrote:
>>>> Dear Josh, dear all,
>>>> Thanks you for your kind answer. I gave it a try without bigdcd and
>>>> it didn't really improve the situation. I have the impression that
>>>> even the centering is not working properly. Indeed when running
>>>> only the first command:
>>>> pbc wrap -compound fragment -center com -centersel "segname A" -now
>>>> -sel "protein"
>>>> Segment A isn't in the middle of my box. Segment E is and still
>>>> moving quite a lot. I do not understand why the centering algorithm
>>>> would allow such a variation in the position of the center of mass
>>>> of the selection neither why segE is centered instead of segA.
>>>> Although since I have an homopentamere I cannot pick the largest
>>>> one as Josh suggested.
>>>> Bests,
>>>> NM
>>>> On 02/19/2016 04:50 PM, Josh Vermaas wrote:
>>>>> Hi Nicholas,
>>>>> I've never done it with bigdcd, but another alternative is a set
>>>>> of two wrap commands. I think unwrap depends on a previous set of
>>>>> coordinates to be loaded, so I'm not sure what it would even do
>>>>> when bigdcd only loads one frame at a time.
>>>>> #This gets the protein together into one group, assuming each
>>>>> chain is its own segment, and isn't too big relative to the
>>>>> periodic box
>>>>> pbc wrap -compound fragment -center com -centersel "segname PA"
>>>>> -now -sel "protein"
>>>>> #This step is optional, and recenters the lipids and waters around
>>>>> the protein that is put back together.
>>>>> pbc wrap -compound fragment -center com -centersel "protein" -now
>>>>> Of course, you'd need to adjust the "segname PA" selection to just
>>>>> pick one segment of the multimer, preferably the largest one.
>>>>> -Josh Vermaas
>>>>> On 02/19/2016 08:30 AM, Nicolas Martin wrote:
>>>>>> Dear users,
>>>>>> I recently run a simulation in NAMD of a pentameric membrane
>>>>>> protein using the wrapping option. Even tough the water and
>>>>>> membrane are correctly wrapped, the protein diffuse in the
>>>>>> simulation box and end ups crossing the periodic boundaries.
>>>>>> Doing so, the protein is not kept full, but 2 chains over 5 jump
>>>>>> on the other side of the box. The wrapping in namd is made so
>>>>>> there is no long bonds and only full chains move to the other
>>>>>> side of the box.
>>>>>> I need all the chains to be put back together at the center of
>>>>>> the box for further analysis.
>>>>>> I tried to follow the documentation for doing so and the best I
>>>>>> could end up with is a protein more or less (the com seems to be
>>>>>> moving significantly) well centered in the box and several frames
>>>>>> over a long trajectory with stretched bonds. Here is the routine
>>>>>> I used over all trajectory frames:
>>>>>> pbc unwrap -sel protein -now
>>>>>> pbc wrap -compound res -center com -centersel "protein" -now
>>>>>> I also used bigdcd (that's why the option -now and not -all was
>>>>>> used above) for reading trajectories and wrote wrapped dcds every
>>>>>> 1000 frames to avoid memory problems (otherwise it's a ~30GB
>>>>>> trajectory).
>>>>>> I also tried using the Join keyword on the first frame which had
>>>>>> no significant effect.
>>>>>> What procedure would you advice me to use in order to get a
>>>>>> perfectly re-centered and wrapped trajectory in the case of my
>>>>>> multi-chains system?
>>>>>> Thanks you in advance for your help,
>>>>>> NM