VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jan 26 2010 - 15:39:18 CST

On Tue, Jan 26, 2010 at 4:31 PM, Mert Gür <gurmert_at_gmail.com> wrote:
> Dear Axel,
> As you sugested I used the following command in order to center my cell
> around the protein.
>
> pbc wrap -center protein -first 0 -last 3000
>
> Unfortunately it looks funny. There are long tube like bonds everywhere. I
> wonder what is wrong with it? On the other hand when I plot the number of

those are due to bonds where one atom has been moved and the other has not.

> hydrogen bonds among water and protein they seem to fluctuate around a value
> which was not the case before (Which is good).
> Can you please tell me if I am doing something wrong or are these long
> tubelike structures normal?

you have to read the pbctools documentation properly.

by default pbc wrap applies periodic boundaries
on a per atom basis. have a look at the -compound flag.

axel.

> Best,
> Mert
>
>
>
>
> On Mon, Jan 25, 2010 at 4:55 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Mon, Jan 25, 2010 at 8:50 AM, Mert Gür <gurmert_at_gmail.com> wrote:
>> > Dear Leonardo,
>> > I have read and tried the link you posted.
>> > I think there have been an misunderstanding. Let's say 1/3th of my
>> > protein
>> > is outside the water box (Not visually wrapped arround to the other
>> > side)
>> > and the rest 2/3th is inside of it. So this 1/3th of my protein is
>> > wiggling
>> > outside the box (Not on the other side). So there seem to be no water
>> > molecules around it.
>>
>> so where is the problem?
>>
>> you use pbc wrap and give it the center of mass of the protein as a
>> reference point for the center. then your protein should always be
>> surrounded by water molecules. if not, you have used too few waters
>> or made a mistake.
>>
>> cheers,
>>   axel.
>>
>>
>>
>> > Best,
>> > Mert
>> >
>>
>>
>> --
>> Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
>> Institute for Computational Molecular Science
>> College of Science and Technology
>> Temple University, Philadelphia PA, USA.
>
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.