VMD-L Mailing List

From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Mon Feb 22 2016 - 14:52:32 CST

Hi Nick,

A good way to check if pbc box is defined would be to type this in TkConsol

molinfo top get a

(you could also do "molinfo top get b" or "molinfo top get c")

a, b, c are defined as the X,Y,Z dimensions of your PBC box. If they are
not set, it will show 0.000

Best,
Chitrak.

On Fri, Feb 19, 2016 at 1:14 PM, Nicolas Martin <nicolasmartin973_at_gmail.com>
wrote:

> 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.
>
> Nick
>
>
> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>