[gmx-users] links warnangles

[Justin A. Lemkul]

Dimitris Dellis wrote:
> Hi.
> There is an issue with constraints.
> H atom position is not uniquely defined with the constraints you use.
> Try these constraints (substitute symbols with numbers)
> 
> 1       2    1       rC-H
> 1       3    1       rC-CL
> 1       4    1       rC-CL
> 1       5    1       rC-CL
> 2       3    1       rH-CL
> 2       4    1       rH-CL
> 3       4    1       rCL-CL
> 3       5    1       rCL-CL 
> 4       5    1       rCL-CL 
> 

I suggested this solution long ago, but Berk said it was an incorrect approach:

http://redmine.gromacs.org/issues/359

-Justin

> DD
> 
> 
> On 02/02/2011 06:20 PM, vferrario at units.it wrote:
>> The dynamic works, but I still have the same problems with 
>> minimization...
>>
>>
>> "Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>>
>>>
>>>
>>> vferrario at units.it wrote:
>>>> Ok and which definition have you used? the previous one with 5 atom 
>>>> for molecule?
>>>>
>>>
>>> Yes.
>>>
>>> -Justin
>>>
>>>> "Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>>>>
>>>>>
>>>>>
>>>>> vferrario at units.it wrote:
>>>>>> Just the last thing... can you copy your mdp file? I think I'm 
>>>>>> having some problems also with that... Thanks.
>>>>>>
>>>>>
>>>>> For EM, I used the .mdp file you posted in your first message and 
>>>>> added the line "continuation = yes."  For MD, I changed nstlist 
>>>>> from 100 to 5.
>>>>>
>>>>> -Justin
>>>>>
>>>>>> Valerio
>>>>>>
>>>>>>
>>>>>> "Justin A. Lemkul" <jalemkul at vt.edu> ha scritto:
>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> Justin A. Lemkul wrote:
>>>>>>>
>>>>>>> <snip>
>>>>>>>
>>>>>>>> I've obtained a stable trajectory for a single CHCL3 molecule.  
>>>>>>>> By setting "continuation = no" (so that constraints are not 
>>>>>>>> solved before step 0) in the em.mdp file, and then reducing 
>>>>>>>> nstlist to 5 in md.mdp, I
>>>>>>>
>>>>>>> Ack, this should be "continuation = yes."  Sorry for the 
>>>>>>> confusion.  I will copy from my .mdp file...I will copy from my 
>>>>>>> .mdp file... :)
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> -- 
>>>>>>> ========================================
>>>>>>>
>>>>>>> Justin A. Lemkul
>>>>>>> Ph.D. Candidate
>>>>>>> ICTAS Doctoral Scholar
>>>>>>> MILES-IGERT Trainee
>>>>>>> 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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>>>>>>
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>>>>>>
>>>>>>
>>>>>
>>>>> -- 
>>>>> ========================================
>>>>>
>>>>> Justin A. Lemkul
>>>>> Ph.D. Candidate
>>>>> ICTAS Doctoral Scholar
>>>>> MILES-IGERT Trainee
>>>>> 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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>>>>
>>>
>>> -- 
>>> ========================================
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> 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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>>
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> 

-- 
========================================

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

========================================