[gmx-users] Coordinates change after minimization

[Mark Abraham]

Ms. Aswathy S wrote:
> But i am in a situation like the minimization doesn't make any change in the energy and it convergeing at 15 th step each time. So further minimization is not possible. Can you plz check the em.mdp file and tell me whetehr I have given any wrong  parameter?

There's nothing there that would cause a problem. So long as nothing in 
the .log file looks amiss, you can probably start equilibrating.

Mark

> ----- Original Message -----
> From: "XAvier Periole" <x.periole at rug.nl>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Saturday, June 20, 2009 7:16:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
> Subject: Re: [gmx-users] Coordinates change after minimization
> 
> 
> 
> 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.
>> Husargatan 3, Box 596,      75124 Uppsala, Sweden
>> phone:    46 18 471 4205        fax: 46 18 511 755
>> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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