[gmx-users] error during energy minimization

[Itamar Kass]

   Dear Shailza,
                             I was wrong, if you get an error regarding  
pressure coupling you probably do MD and not energy minimization.  In  
order to do EM change the line:
integrator    =    md
at the em.mdp file to
integrator    =    cg


               Good luck.


On Feb 22, 2005, at 11:23 AM, shailza singh wrote:

>
>
> hi,
> I am using Berendsen pressure coupling.
>
> shailza.
>
>
>
>
>  --- Itamar Kass <ikass at cc.huji.ac.il> wrote:
>>
>>    Can you state what is your presser coupling
>> method?  Probably
>> something is wrong with the pressure coupling.  In
>> case not, you can
>> try to minimize your system using other coupling
>> parameters.
>>          Kass.
>>
>>
>> On Feb 21, 2005, at 6:16 PM, shailza singh wrote:
>>
>>>
>>> hi all,
>>> i am novice to GROMACS and trying to perform
>> energy
>>> minimization for my protein.But during mdrun i
>>> encountered the following error:Back Off! I just
>>> backed up step177.pdb to ./#step177.pdb.1#
>>> Wrote pdb files with previous and current
>> coordinates
>>>
>>> Step 179  Warning: pressure scaling more than 1%,
>> mu:
>>> inf inf inf
>>> Warning: Only triclinic boxes with the first
>> vector
>>> parallel to the x-axis and the second vector in
>> the
>>> xy-plane are supported.
>>>          Box (3x3):
>>>             Box[    0]={         inf,
>> nan,
>>>       nan}
>>>             Box[    1]={         nan,
>> inf,
>>>       nan}
>>>             Box[    2]={         nan,
>> nan,
>>>       inf}
>>>          Can not fix pbc.
>>> Fatal error: ci = -1 should be in 0 .. -1 [FILE
>>> nsgrid.c, LINE 218]
>>>
>>> Please help
>>> Thanking you in advance
>>> shailja
>>>
>>>
>>
> _______________________________________________________________________
>>
>>> _
>>> Yahoo! India Matrimony: Find your life partner
>> online
>>> Go to: http://yahoo.shaadi.com/india-matrimony
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please don't post (un)subscribe requests to the
>> list. Use the
>>> www interface or send it to
>> gmx-users-request at gromacs.org.
>>>
>>
>>
>> ===========================================
>> | Itamar Kass
>> | The Alexander Silberman
>> | Institute of Life Sciences
>> | Department of Biological Chemistry
>> | The Hebrew University, Givat-Ram
>> | Jerusalem, 91904, Israel
>> | Tel: +972-(0)2-6585194
>> | Fax: +972-(0)2-6584329
>> | Email: ikass at cc.huji.ac.il
>> | Homepage:
>>
> http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
>> ============================================
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the
>> list. Use the
>> www interface or send it to
>> gmx-users-request at gromacs.org.
>>
>
> _______________________________________________________________________ 
> _
> Yahoo! India Matrimony: Find your life partner online
> Go to: http://yahoo.shaadi.com/india-matrimony
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>


===========================================
| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585194
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Homepage:  
http://www.ls.huji.ac.il/~membranelab/itamar/itamar_homepage.html
============================================
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 3952 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050222/ffd9cf06/attachment.bin>