[gmx-users] links warnangles
vferrario at units.it
vferrario at units.it
Thu Feb 3 11:07:00 CET 2011
Sorry, but changing the definition and using the other suggested by
Dimitris doesn't change the results, I still have the same problem in
minimisation...
Valerio
Dimitris Dellis <ntelll at gmail.com> ha scritto:
> 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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>>>>>>>>
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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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>>>
>>
>
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