[gmx-users] segmentation fault on trjconv with deshuf

Lynne E. Bilston l.bilston at unsw.edu.au
Mon Jun 17 01:11:14 CEST 2002

At 09:49 AM 14/06/2002 +0200, Anton Feenstra wrote:
>Lynne E. Bilston wrote:
>>Hi all,
>>I've used the -shuffle -sort options for a longish run (1ns), and now I 
>>want to continue the run from that endpoint. Of course, grompp complaints 
>>about the atom names not matching due to the shuffling/sorting.
>>Any ideas - either on how to continue my run or the core dump in trjconv?
>Continuing is simple: don't use trjconv/grompp, but tpbconv in stead.
>It will read your .trr (shuffled) and .tpr (shuffled) and writes a new
>.tpr (also shuffled) which you can feed to mdrun. Note, that tpbconv by
>default does not modify the original 'ending time' of the run, so you
>will probably need to use the -extend or -until options.
This works if I want to extend the same run, but if I was doing an 
equilibration run and wanted to change the parameters, then I presume I 
have to use grompp/trjconv?



Lynne E. Bilston, PhD
Senior Scientist, Prince of Wales Medical Research Institute, and
Conjoint Associate Professor, Faculty of Medicine, University of New South 
Barker St, Randwick, NSW 2031 Australia
Tel: +61-2-9382-7924	Fax: +61-2-9382-2643

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