VMD-L Mailing List

From: Nicolas Martin (nicolasmartin973_at_gmail.com)
Date: Fri Feb 19 2016 - 12:04:18 CST

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
>>>>
>>>
>>
>