From: johan strumpfer (johan.ks.uiuc_at_gmail.com)
Date: Fri Jun 03 2011 - 12:09:55 CDT
Hi Werner,
To wrap everything into one unit cell around the protein I usually use
something like
pbc wrap -all -sel "not protein" -compound res -center com -centersel "protein"
You might want to add -shiftcenter {$x $y $z} to the above command
(where you will have to work out what x y z is) if the substrate is
near a cell boundary to make it appear closer to the protein.
Hope this helps,
Johan
----------------------------------------------------------------
Johan Strumpfer (johanstr_at_ks.uiuc.edu)
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
On Thu, Jun 2, 2011 at 5:18 AM, Werner Crous <crous.werner_at_gmail.com> wrote:
> 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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