Dear Pinky,
Take a look at the MULTI_RMSD as the &colvar option, you have an example at the figure 23.5.
Best,
Fabian
Fabian Glaser PhD
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web
https://lokey.technion.ac.il/bioinformatic-knowledge-unit/
Tel +972 (0) 4 8293701
> On 16 Jan 2021, at 4:01, Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> 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 <mailto: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 Sat Jan 16 2021 - 07:00:03 PST
