[gmx-users] center of mass motion

Florian Haberl Florian.Haberl at chemie.uni-erlangen.de
Wed Jan 4 12:16:40 CET 2006


On Wednesday 04 January 2006 11:22, herbst at fhi-berlin.mpg.de wrote:
> Hi all,
> my protein is jumping out of the box during the simulation. I tried to
> center it in the box using trjconv -pbc inbox -center, but when I look at
> the new trajectory, it is still leaving the box and I can't watch it.
> Am I doing something wrong ?
Take a reference strucuture which is inside the box, normally the minimized em 
or pr file. ( trjconv -s file. ...)

> And how can I constrain the center of mass motion in the simulation ?

> Thanks,
> Anna
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 Florian Haberl                        
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de

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