[gmx-users] Gromacs Tutorial by Justin

[Faezeh Pousaneh]

Dear Justin

One more question please,
Do we need to have constraint in this model of CO2?  Isn't it so that we
have fixed the bond lengths and angles (180) in the topology by this method?

I run 2 simulations, one with constraints = all-angles  and the other
with constraints
= all-bonds, I get different results from them. Why?



Best regards


On Wed, Mar 7, 2018 at 2:54 PM, Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> Thank you.
>
>
> Best regards
>
>
> On Wed, Mar 7, 2018 at 1:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/7/18 6:24 AM, Faezeh Pousaneh wrote:
>>
>>> Dear Justin,
>>>
>>> I have 2 questions regarding your tutorial on Carbon Dioxide in this
>>> link:
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx
>>> -tutorials/vsites/index.html
>>>
>>> 1- I see that in your simple simulation you use no boundary conditions,
>>> pbc=no, should it be always so for this model?
>>>
>>> 2- You use
>>>   comm-mode = angular,
>>> is that necessary?
>>>
>>
>> The simulation is a simple gas-phase system, which does not use PBC and
>> hence requires angular COM motion removal.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>
>> ==================================================
>>
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>