feenstra at chem.vu.nl
Mon Sep 29 08:59:00 CEST 2003
> On Fri, 2003-09-26 at 03:55, Dallas Warren wrote:
>>>just periodic boundary conditions.
>>OK, thought that might be the other possible thing causing problems.
>>This pops up a bit I have noticed. For the developers, is it possible
>>to integrate support of the pbc into these scripts? I know there are
>>a few tricks to get them supporting the pbc, but have no idea if it
>>will fit in with the various GROMACS scripts. A colleague here has
>>implemented it into a package of Perl scripts that he has written to
>>manipulate various simulation files.
> It is *possible* of course. One would just have to call the routines
> that are already in trjconv. But it's work...
You can still first do it 'manually' with trjconv, with the added advantage
that it only has to be done once, and you can check if it is done the way
you expect it to. Having said that, the last time I tried either -pbc nojump,
or the 'cluster' option, it didn't work the way I expected (but I also did
not have time then to get to the bottom of it).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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