From: Josh Vermaas (
Date: Fri Feb 19 2016 - 12:10:53 CST

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. :(

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