[gmx-users] center of mass motion

[herbst at fhi-berlin.mpg.de]

hi,
I tried it with my starting geometry as a reference structure, but the
protein still vanishes after 300 ps. What can I do ? Can I somehow fix the
protein in the box during the simulation ?

Thanks,
Anna


> hi
>
> 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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>
> Greetings,
>
> Florian
>
> --
> -------------------------------------------------------------------------------
>  Florian Haberl
>  Computer-Chemie-Centrum
>  Universitaet Erlangen/ Nuernberg
>  Naegelsbachstr 25
>  D-91052 Erlangen
>  Mailto: florian.haberl AT chemie.uni-erlangen.de
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