[gmx-users] error about pbc

[Justin Lemkul]

On 1/26/13 8:17 PM, Kieu Thu Nguyen wrote:
> Thank Tsjerk so much !
> But after being minimized 50000 steps and equilibrated 90 ns, there are
> some bonds in the system that rotate more than 30 degrees.
> I applied tips for blew up system as you advised. But the system does not
> achieve balance.
> Should i carry out more many steps for minimization ? or minimize many
> times ? to get more equilibrated system.
>

I would say that 50000 steps of minimization is far more than is normally 
necessary.  What Fmax do you achieve at the end of EM?  What is in the system? 
What is in your .mdp file?  Systems can randomly crash if the model physics 
breaks due to incorrect .mdp settings or an unstable topology.

-Justin

> On Thu, Jan 24, 2013 at 11:13 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:
>
>> Hi KT,
>>
>> This is caused by another problem. Your system blew up. Check messages
>> before this one, and check the log for LINCS warnings.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Thu, Jan 24, 2013 at 9:11 AM, Kieu Thu Nguyen <kieuthu2212 at gmail.com
>>> wrote:
>>
>>> Dear All,
>>>
>>> My MD simulation  has an error
>>>
>>> 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]={         nan,          nan,          nan}
>>>              Box[    1]={         nan,          nan,          nan}
>>>              Box[    2]={         nan,          nan,          nan}
>>>           Can not fix pbc.
>>>
>>> I searched on Gromacs-errors web, but i did not see this error.
>>> How can i fix it ?
>>>
>>> Thanks and regards,
>>> KT
>>> --
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>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Biocomputing Group
>> Department of Biological Sciences
>> 2500 University Drive NW
>> Calgary, AB T2N 1N4
>> Canada
>> --
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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