From: Haleh Abdizadeh (halehabdi_at_sabanciuniv.edu)
Date: Wed Sep 25 2013 - 15:06:19 CDT
Thank you all...
On Wed, Sep 25, 2013 at 10:53 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> yes that is correct. If you want to see it with the protein in the middle
> you can use the pbctools plugin commands in VMD.
>
> For instance, in the TKConsole, you could enter the following commands:
>
> pbc unwrap
> pbc wrap -centersel "protein" -center com -compound residue -all
>
> I'm not actually confident you need to unwrap it first, but at any rate,
> the above will work to shift where the periodic box is, such that you're
> protein is now in the middle. It assumes that VMD already has the periodic
> box values, which it should have automatically if you're loading an NAMD
> DCD trajectory.
>
> ~Aron
>
>
> On Wed, Sep 25, 2013 at 3:00 PM, Haleh Abdizadeh <
> halehabdi_at_sabanciuniv.edu> wrote:
>
>> Because of the periodic boundary condition? I mean a small part of
>> protein comes out of water box but i suppose it should enter the water box
>> just next to it. Am I right?
>>
>>
>> On Wed, Sep 25, 2013 at 8:44 AM, Norman Geist <
>> norman.geist_at_uni-greifswald.de> wrote:
>>
>>> Nothing to worry about and no need to rerun the simulation.****
>>>
>>> ** **
>>>
>>> Norman Geist.****
>>>
>>> ** **
>>>
>>> *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *Haleh Abdizadeh
>>> *Gesendet:* Dienstag, 24. September 2013 16:53
>>> *An:* namd-l_at_ks.uiuc.edu
>>> *Betreff:* namd-l: cell origin problem****
>>>
>>> ** **
>>>
>>> Dear all,****
>>>
>>> I have made a mistake in entering cell origin coordinates in restart
>>> conf file. When I play the movie of trajectories I do not see any problem
>>> in my protein but I am not sure if my results are correct or not. I know
>>> cell origin is not the center of mass of the protein but center of the
>>> water box so could anyone tell me if it is necessary for me to start the
>>> whole simulation again?****
>>>
>>> Best wishes,****
>>>
>>> Haleh****
>>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
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