[gmx-developers] trjconv defaults

David Mobley dmobley at gmail.com
Fri Oct 17 15:35:24 CEST 2008

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?)


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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