Re: diffusion of protein into water box

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 25 2013 - 07:13:57 CST

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On Mon, Nov 25, 2013 at 9:30 AM, Ramin Ekhteiari <ramin_ekh_at_yahoo.com> wrote:
> My problem is solved when I use this commands
>
> **pbc wrap -centersel "protein" -center com -compound residue -all**

which means, that there wasn't really a problem at any time. your
trajectory is still the same, only that you have picked a different
point of reference and different periodic images for the atoms of
certain residues.

axel.

> Ramin
>
>
> On Sunday, November 24, 2013 4:26 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> On Sun, Nov 24, 2013 at 3:21 PM, Ramin Ekhteiari <ramin_ekh_at_yahoo.com>
> wrote:
>> Is it reasonable? ( diffusion of protein ).
>
> why should it not be reasonable? have you check the (many!)
> discussions on that same subject in the mailing list archives? might
> be enlightening... ;-)
>
>> But when protein cross the
>> boundary of the box, the periodic images will
>> interact with themselves affecting the outcome of the simulation.
>
> i don't understand what this is supposed to mean.
>
> axel.
>
>>
>> Ramin.
>>
>>
>>
>>
>>
>> On Sunday, November 24, 2013 4:14 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> wrote:
>> On Sun, Nov 24, 2013 at 3:06 PM, Ramin Ekhteiari <ramin_ekh_at_yahoo.com>
>> wrote:
>>> Hi,
>>>
>>> I did a MD for a protein at a water box via NAMD, but during simulation
>>> the
>>> protein diffuse along the box and cross the boundary.
>>>
>>> Would be grateful for any help.
>>
>> help to do what?
>>
>> axel.
>>
>>
>>>
>>> Cheers,
>>> Ramin
>>
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> International Centre for Theoretical Physics, Trieste. Italy.
>
>>
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.

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