[gmx-users] center of mass motion

[leafyoung81-group at yahoo.com]

check 3.3's trjconv.

----- Original Message ----
From: herbst at fhi-berlin.mpg.de
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, January 04, 2006 8:12:06 PM
Subject: Re: [gmx-users] center of mass motion

trjconv does not know this option

> use trjconv -center tric -f in.xtc -o out.xtc
>
> Yang Ye
> Nanyang Technolgoical University, Singapore
>
> ----- Original Message ----
> From: Florian Haberl <Florian.Haberl at chemie.uni-erlangen.de>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Wednesday, January 04, 2006 7:16:40 PM
> Subject: Re: [gmx-users] center of mass motion
>
> 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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>
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