[gmx-users] links warnangles

[vferrario at units.it]

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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