[gmx-users] Coordinates change after minimization

[XAvier Periole]

On Jun 20, 2009, at 15:30, "Ms. Aswathy S" <aswathys at amritapuri.amrita.edu 
 > wrote:

> using the g_confrm command the RMSD of the protein is 0 (Root mean  
> square deviation after lsq fit = 4.14581e-08). It means the  
> structure doesn't have a major change ultimately.. Please correct me  
> if I am wrong..
You are correct.
> Can I move ahead with this minimization?
However this value is really small, which suggests that the  
minimization did actually about nothing. This a bit too nothing!

Of I were you I would check that you actually used g_confrm the right  
way or indeed performed a minization.
>
> Dept. Biotechnology
> Ext. 3108
>
> ----- Original Message -----
> From: "David van der Spoel" <spoel at xray.bmc.uu.se>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai,  
> Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] Coordinates change after minimization
>
> Justin A. Lemkul wrote:
>>
>>
>> Ms. Aswathy S wrote:
>>> Hi,
>>>
>>> After minimizing the protein -ligand complex, the co-ordinates have
>>> changed
>>> drastically.My idea about minimization was the coordinates will have
>>> minute
>>> changes only. In this case my protein is completely transferring  
>>> to a new
>>> co-ordinates.Is that reasonable.??
>>
>> The amount of change will depend on the quality of the initial model.
>> If large changes need to be made, they can be.  If the entire  
>> protein is
>> moving, then perhaps the box has not been prepared correctly, and the
>> translation is caused by a periodic jump.  Have a look at the output
>> (not just the coordinates) and see if you can deduce what's going on.
>>
> Try running g_confrms to see whether they really are very different.
>
>> -Justin
>>
>>>
>>> Thanks, Aswathy Dept. Biotechnology Ext. 3108
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>>
>
>
> -- 
> David.
> ________________________________________________________________________
 

> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
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