[gmx-developers] trjconv defaults

[David van der Spoel]

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?

> 
> Cheers,
> 
> Erik
> 
> 
> On Oct 17, 2008, at 11:00 AM, Berk Hess wrote:
> 
>> Hi,
>>
>> It would be nice to somehow automatically have trjconv fix molecules,
>> but there are several issues.
>>
>> 1) trjconv will then by default need a tpr file
>> 2) for trajectory conversion you don't want this in general
>> (automatically modifies your trajectories and makes things slower)
>>
>> I think that ideally trjconv should do -pbc mol automatically when 
>> writing
>> pdb or gro. But that is confusing, since the settings of options will 
>> then
>> depends on  the output format.
>>
>> Berk
>>
>>
>> David van der Spoel wrote:
>>> Hi,
>>>
>>> shall we set the trjconv defaults to -pbc mol -ur compact ?
>>> Even I get fooled when dumping a pdb file and suddenly noticing that 
>>> it is broken.
>>>
>>> Cheers,
>>
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> 
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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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