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
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Received on Sat Jul 25 2020 - 21:30:03 PDT
