VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Nov 11 2014 - 19:13:00 CST

Hey,

You are mixing two different things - boundaries and the wrapping.
You can skip on the wrap command and the atoms/chains/molecules (depending
on what your system has - wont be wrapped. Consequently if you have wrapped
it already there is unwrapping available as a part of the PBC plugin (it
isn't specific).

for your specific version look for unwrap in the plugin you have working
for you here:

https://github.com/olenz/pbctools/downloads

moreover a chain will only split if they are two chains (in terms of their
chain IDs). i.e. with wrapALL and wrapNearest activated If one chain
completely moves out it will get wrapped. Depending on what you want you
can look into these.

Hope this helps.

Good Luck.

Best,
/A

On Wed, Nov 12, 2014 at 1:12 PM, M K <mahyar.karimi20_at_gmail.com> wrote:

> Hi,
>
> I face a similar problem.
> I simulate a polymer chain in water. I can select this chain using
> "protein" selection. During the simulation, it moves and goes beyond the
> boundaries of the box, and enters from the other side due to the periodic
> nature.
> I want to keep this polymer chain always in the center of the cubic box; a
> good try is probably keeping the center of mass of the polymer chain in the
> center of the box. I tried the following code and some other variations,
> but they don't work; the chain is again split into parts when going beyond
> the boundaries:
>
> *pbc wrap -all -sel "protein" -center boundingbox -centersel "protein"*
>
> Can someone please help? What is the problem with the code I'm using?
>
> On Tue, Sep 30, 2014 at 12:14 AM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
>> Hi Phan,
>>
>> You can use the PBCtools plugin (
>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/) to rewrap your
>> trajectory. If you just care about the hydrogen bonds between proteins,
>> what you should be able to do is use something like this:
>>
>> pbc wrap -all -sel "protein" -center com -centersel "some atomselection
>> text that only picks out one of the two protein copies"
>>
>> Then the selected protein will be near the center, and any of the atoms
>> involved in hydrogen bonding should be inside the same unit cell. Read the
>> documentation, and play around to see which combination of options you
>> prefer.
>>
>> -Josh Vermaas
>>
>>
>> On 09/29/2014 08:09 AM, Vy Phan wrote:
>>
>> Dear Vmd users,
>> My systems for MD simulations included 2 protein, but after 50ns of
>> trajectory, one protein go out side the water box (sometimes comeback). I
>> knew why this phenomenon happened but when I do not know how to analyze the
>> result.
>> I have problem when I calculated hydrogen bonds between two protein.
>> Because of the boundary condition, the result of hydrogen bonds is not
>> right. How can I solve this problem?
>>
>> Thank a lot and best regards,
>>
>> Phan Vy
>>
>>
>>
> 

-- 
Best,
/A