Re: PBC

From: Werner Crous (crous.werner_at_gmail.com)
Date: Thu Jun 02 2011 - 04:18:38 CDT

Hi Johan

I just realised that the frames for which it is not working is the same as
the original ones where the substrate was 72A away from its original
position. Now it is just 21A away, but what should I do to get it in the
correct position, because it still fluxuates from in the enzyme and then 21A
away even when I applied the unwrap.

Regards
Werner

On Thu, Jun 2, 2011 at 11:05 AM, Werner Crous <crous.werner_at_gmail.com>wrote:

> Hi Johan
>
> Thank you. I tried to use PBCTools. I specified a variable of the fragments
> I would like to keep together. I then used pbc join res -ref $keeptogether
> and then pbc unwrap. I hope I did it correctly. My substrate is now in the
> correct position for most of my frames. there are some where is is still
> somewhat away. The water molecules are smeared.
>
> Werner
>
>
>
> On Wed, Jun 1, 2011 at 7:19 PM, johan strumpfer <johan.ks.uiuc_at_gmail.com>wrote:
>
>> HI Werner,
>>
>> This is indeed just an imaging issue. To re-wrap the output it is easiest
>> to use the PBCtools plugin in VMD. You can then wrap the resulting
>> output either by segment or by residue (see the documentation:
>> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/). As far as I know,
>> namd wrap's dcd output by residue if you specify wrapAll, wrapNearest
>> or wrapWater (see http://www.ks.uiuc.edu/Research/namd/2.8/ug/node33.html
>> ).
>>
>> The cut-off that you are referring to I presume is the charmm CUTIM
>> parameter? If I remember correctly, this is used to set the maximum
>> distance for generating the pairlist. The equivalent parameter in namd
>> is pairlistdist. See
>> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node39.html for more info.
>>
>> Groete,
>> Johan
>>
>>
>> > On Wed, Jun 1, 2011 at 6:09 AM, Werner Crous <crous.werner_at_gmail.com>
>> wrote:
>> >> Dear NAMD-users
>> >>
>> >> I have a problem with imaging in NAMD. I used a truncated octahedron
>> within
>> >> the NVT ensemble. What happened was that after 12ns the protein only
>> >> partially moved out of the truncated octahedron, but my one substrate
>> was
>> >> imaged right to the other side of the box. This then looks as if the
>> >> substrate moved out of the protein, but I assume it is just the
>> imaging. The
>> >> susbstrate is imaged differently to the protein. As a CHARMM user, I
>> know
>> >> that one can specify if you want the imaging to happen by segment or by
>> >> residue, but in NAMD I am not aware of such options. How does imaging
>> work
>> >> in NAMD for a TOH and what is the cutoff for the minimum imaging
>> convention?
>> >>
>> >> Thank you in anticipation.
>> >>
>> >> Best regards
>> >> Werner
>> >>
>> >>
>> >>
>> >> --
>> >> Werner Crous
>> >> Scientific Computing Research Unit
>> >> University of Cape Town
>> >> Rondebosch 7701
>> >> South Africa
>> >> Phone: +27 21 650 2530 (O)
>> >> Fax: +27 21 686 4333
>> >> http://scru.uct.ac.za
>> >> http://scientificomputing.com
>> >>
>> >
>>
>
>
>
> --
> Werner Crous
> Scientific Computing Research Unit
> University of Cape Town
> Rondebosch 7701
> South Africa
> Phone: +27 21 650 2530 (O)
> Fax: +27 21 686 4333
> http://scru.uct.ac.za
> http://scientificomputing.com
>

-- 
Werner Crous
Scientific Computing Research Unit
University of Cape Town
Rondebosch 7701
South Africa
Phone: +27 21 650 2530 (O)
Fax: +27 21 686 4333
http://scru.uct.ac.za
http://scientificomputing.com

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