[gmx-developers] trjconv defaults

[David Mobley]

That's a good idea. Anything to make this more transparent would help, I think.

David


On Fri, Oct 17, 2008 at 10:37 AM, Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
> We could implement a proper solution for this.
>
> An option one would be:
> -pbc nojump
> center on protein
> -pbc mol
> But then all in one call of trjconv
>
> Berk
>
>
> David Osguthorpe wrote:
>>>
>>> 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?)
>>>
>>>
>>
>> Id also like to second this - the right magic trick to get ligands
>> to be in their binding site is somtimes quite complicated
>> - cluster has worked for me but also gets into an infinite loop sometimes
>> - Im still running 3.3.1 to maintain numerical consistency - ie.
>> I can reproduce trajectories at the binary level
>>
>> David
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