From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Nov 24 2013 - 08:24:47 CST
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.
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