[Bulk] [gmx-users] RMSD graph

[Diego Enry]

Like Yang Ye said, molecule is likely out of the box (just fix PBC).
This also happens when you don't know how to continue a broken
simulation (check the WIKI on gmx website)
I had this PBC issue many times. What works over here to make things easier is:

Be sure that in the reference frame "-s" the molecule is in the box.

1) remove pbc
trjconv -s md.tpr -f md.xtc -o md.nojump.xtc -pbc nojump  (also remove
water since you don't need them for g_rms)

2) check with "vmd" to see if it worked

3) fit the trajectory  ( and keep for animations :) )
trjconv -s md.tpr -f md.nojump.xtc -o md.nojump.fit.xtc -fit rot+trans

4) check the result with "vmd", it looks beautiful

5) g_rms -f  md.nojump.fit.xtc .....

Have fun,
Diego Enry.

On Wed, Jun 18, 2008 at 2:55 AM, Yang Ye <leafyoung at yahoo.com> wrote:
> Quite likely, it is due to part of molecule moving "out of box". Also, the
> molecule could be of multiple chain.
>
> So you need to find a way to put the whole molecule in one piece. Try
> various options from trjconv -pbc. If it is DNA, a trick is to define one
> chain as an index group and then center that group.
>
> Regards,
> Yang Ye
>
> Anamika Awasthi wrote:
>>
>>
>> Dear All,
>>       Please tell, what should I predict from this graph?
>>       I can understand this is normal type of graph.
>>       Sorry for inconvenience, but I want to ask some questions,
>> my this job crashed many time, because of power shut down and I had to
>> restart this again and again, I used tpbconv for the same.
>> but now when I was trying to get rmsd plot from my running job..its not
>> reading the tpr file, which I got from tpbconv , its reading previous tpr
>> file.
>> Is it okey?
>>  Thanks in advance
>>         Anamika
>>
>>
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.