[gmx-users] links warnangles

[Justin A. Lemkul]

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

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