Hi,
Do you know how to pull a group of atoms towards a fixed atom?
Thank you.
Sincerely,
Pinky
On Sat, Jul 25, 2020 at 11:16 PM Pinky Mazumder <pmazumder67.gmail.com>
wrote:
> Thank you again! I will try in this way.
>
>
> Sincerely,
> Pinky
>
> On Sat, Jul 25, 2020 at 9:52 PM Vishal Singh <vishal.chemistry5.gmail.com>
> wrote:
>
>> Dear Pinky
>> The formula you are using for calculating the force is correct, but once
>> you can try to plot the Force_vs_distance curve from the output files of
>> the SMD simulations. If you are using AMBER tutorial, the asmd_1.work.dat.*
>> files give the distance (it is vt=displacement in your calculation), actual
>> distance, force (I think this is your force, f) and work. You can extract
>> the first column (.i.e. vt) and third column (.i.e. force, f) from above
>> files and plot distance_vs_Force and see if this matches with your plot or
>> not.
>>
>> Thanks.
>>
>> VISHAL SINGH
>>
>> On Sun, Jul 26, 2020 at 2:37 AM Pinky Mazumder <pmazumder67.gmail.com>
>> wrote:
>>
>>> Hi Vishal,
>>>
>>> Thank you so much.
>>>
>>> I am facing another problem. When I have plotted the shear force vs
>>> displacement curve, I am getting some negative value of forces. However, in
>>> the previous paper, they have plotted the curve using all the positive
>>> force values.
>>>
>>> Nanoscale toughening mechanism of nacre tablet ,Ning Zhang
>>> <https://pubmed.ncbi.nlm.nih.gov/?term=Zhang+N&cauthor_id=26327454> , Shengfeng
>>> Yang <https://pubmed.ncbi.nlm.nih.gov/?term=Yang+S&cauthor_id=26327454>
>>> , Liming Xiong
>>> <https://pubmed.ncbi.nlm.nih.gov/?term=Xiong+L&cauthor_id=26327454> , Yu
>>> Hong <https://pubmed.ncbi.nlm.nih.gov/?term=Hong+Y&cauthor_id=26327454>
>>> , Youping Chen
>>> <https://pubmed.ncbi.nlm.nih.gov/?term=Chen+Y&cauthor_id=26327454> I am
>>> using F=k(vt-x) for the calculation of force. Here, vt=displacement. Am I
>>> correct? If I am not ,could you please help me with this?
>>> What formula should I use for shear force?
>>>
>>> Thanks!
>>>
>>> Regards,
>>>
>>> On Fri, Jul 24, 2020 at 11:40 PM Vishal Singh <
>>> vishal.chemistry5.gmail.com> wrote:
>>>
>>>> Dear Amber Users,
>>>> You cannot directly give the velocity in the input file of SMD. But you
>>>> have to manage accordingly using the input of what distance you are
>>>> stretching the two molecules and for this what is the length of the
>>>> simulation.
>>>> e.g. if you stretch the molecules 5A (angustrom) (e.g. from 16A to 21A)
>>>> in 5ns then the velocity is 5A/5ns i.e. 1A/ns.
>>>> Similarly, for stretching the molecules 25A in 500 ps simulation then
>>>> the velocity is 25A/500ps i.e. equivalent to 50A/ns.
>>>>
>>>
>>>
>>> --
>>> Pinky, Sharmi
>>> AL,US
>>>
>>
>
> --
> Pinky, Sharmi
> AL,US
>
--
Pinky Mazumder
PhD Student
University of Alabama
USA
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Received on Fri Jan 15 2021 - 18:30:02 PST
