Re: PBC

From: johan strumpfer (johan.ks.uiuc_at_gmail.com)
Date: Wed Jun 01 2011 - 12:19:04 CDT

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
>>
>

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