[gmx-users] Coordinates change after minimization

[XAvier Periole]

try to set the value of emtol to about 10000 times smaller !

On Jun 20, 2009, at 4:30 PM, 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?
>
>
> Dept. Biotechnology
> Ext. 3108
>
> ----- 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
>>>> _______________________________________________ gmx-users mailing
>>>> list
>>>> gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search
>>>> the
>>>> archive at http://www.gromacs.org/search before posting! Please
>>>> don't
>>>> post (un)subscribe requests to the list. Use the www interface
>>>> or send it to gmx-users-request at gromacs.org. Can't post? Read
>>>> http://www.gromacs.org/mailing_lists/users.php
>>>>
>>>
>>
>>
>> -- 
>> 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
>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> +++
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> <em_old.mdp>_______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php