[gmx-developers] trjconv defaults

[David van der Spoel]

David van der Spoel wrote:
> David Mobley wrote:
>> 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
>>>
> 
> We should probably implement something where we  do operations on 
> trajectories in the order of the command line. All the operations then 
> have to go into subroutines and we would introduce a loop over the 
> options. In that manner the main loop becomes much simpler, and one 
> could do anything that trjconv can do in go instead of calling it many 
> times. It would be much faster as well.

Oh by the way, we can merge in trjorder and trjcat as well...

> 
> 
> 
>>> 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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> 
> 


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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