[gmx-users] links warnangles

[Dimitris Dellis]

On 02/02/2011 07:47 PM, Justin A. Lemkul wrote:
>
>
> 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
>

In the above suggestion, the number of constraints is 9, as it should be.
One constraint replaced by another in order to keep H position 
definition unique.
Over-constraining gives wrong results.

DD


> -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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>>>>>>
>>>>>> -- 
>>>>>> ========================================
>>>>>>
>>>>>> 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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>>>
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>>
>