[gmx-developers] trjconv defaults

[Tsjerk Wassenaar]

Hi,

I just rewrote the routine for constructing a molecular shaped box and
put it in my trjconv. Much quicker and more streamlined code than the
original implementation :) The new source is attached, and can replace
the existing trjconv.c. It adds a function (molbox), which should
probably be put in pbc.c, but then I'd have more files to change and
to communicate more patchwork here. Also, as it is now, it only works
with PBCcomAtom, which is set to TRUE if -ur is set to molbox. trjconv
-ur molbox will ask for two selections, one to use as the seed for
construction of molecular shaped box, applied to the other.

-ur molbox will allow better representation of solvated systems, as it
can ensure that each atom of the second selection is placed closest to
the first, unlike with -ur compact. Only if the seed touches itself
over the periodic boundaries can 'dry' spots occur. In addition, this
is the best way to make sure a ligand is put in the pocket, as that is
where it will have its minimal distance to the protein.

Feel free to add this to the official version... Polish where
polishing needed, although I would like to hear suggestions for
improvements...

Cheers,

Tsjerk


On Fri, Oct 17, 2008 at 3:35 PM, David Mobley <dmobley at gmail.com> wrote:
> I'm not as up on all of the PBC options here, but I do want to point
> out something that I have recurring problems with: Ligands. In
> particular, when I am simulating a protein-ligand system, I often find
> it hard to get the pbc options to keep the ligand so it appears in the
> binding site in the protein rather than showing an image of the
> ligand. I am sure there are workarounds with the pbc options (cluster
> has worked well for me sometimes) but just another thing to factor
> into the discussion.
>
> I can't even count how many times there are e-mails on the users list
> where people complain that their ligand doesn't stay bound to the
> protein; usually it's pbc problems. (Perhaps it's a good idea to
> actually put a suggestion relating to this in the documentation?)
>
> David
>
>
> On Fri, Oct 17, 2008 at 5:01 AM, Erik Lindahl <lindahl at cbr.su.se> wrote:
>> Hi,
>>
>> On Oct 17, 2008, at 11:44 AM, Berk Hess wrote:
>>
>>> David van der Spoel wrote:
>>>>
>>>> Erik Lindahl wrote:
>>>>>
>>>>> Hi,
>>>>>
>>>>> I agree with Berk here.
>>>>
>>>> OK, fine.
>>>>
>>>>>
>>>>> Another (unrelated) problem occurs when we write e.g. large ion channels
>>>>> with multiple chains - it can be quite nasty to get the chains in the same
>>>>> periodic image without using the clustering option, which right now is
>>>>> horribly slow for large systems...
>>>>
>>>> Doesn't -pb mol combined with centering do the trick?
>>>>
>>> I would say -pbc nojump is the magic option that fixes all this at one and
>>> it fast,
>>> only the solvent will then move out of the box over time.
>>
>> Yes, it works, but you have to process the trajectory 2-3 times to first get
>> the protein whole, then remove translation, and finally get the water in the
>> box ;-)
>>
>> Cheers,
>>
>> Erik
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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