[gmx-users] Periodic boundary problem

[Haberl Florian]

>> >
>> > But
>> > trjconv -s -pbc nojump
>> > should fix the problem when the tpr file given with -s has the correct
>> > complex conformation.
>>
>>So i only need to take an input file with the "correct" look (both dimers
>>together), and then it should work?
>
> Yes.
> That is what the manual page says.
> And that is how I programmed it.
> It has always worked for me.
> If it doesn't work for you, please tell us.
>
>>
>> > Note that your problem is not really a problem, unless you want to
>> make
>> > nice
>> > pictures
>> > or do a visual inspection.
>>
>>So how can i fix it, if i want to make nice pictures or animations?
>
> With the method desdribed above.
> And probably also with the cluster option as mailed by Kay Gottschalk.

I^ll changed my viewer to VMD and tried as you said, now it works perfect,
think gOpenMol got some probs with certain structures.

thx to all

>
> Berk.
>
> _________________________________________________________________
> Hotmail en Messenger on the move
> http://www.msn.nl/communicatie/smsdiensten/hotmailsmsv2/
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>

Greetings,

Florian


------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

------------------------------------------------------------------------