Thank you Sir.
Actually, my system is a sandwich like structure. And, I need to pull/move
the top and bottom layer, to see their interaction among them. I have to
see the shear phenomenon between them, how hydrogen bonds are forming or
breaking between the layers.
Do you have any suggestions how I could do that in AMBER?
Another query, if there is any way to give compressive force in a
system/model to deform the system?
Any suggestions would be much appreciated.
Thanks again!
On Sat, Jan 16, 2021 at 8:16 AM Vishal Singh <vishal.chemistry5.gmail.com>
wrote:
> Dear Pinky
>
> Pulling a group of atoms means you have to attach separate spring for each
> of the SMD atom (which atomes you have to pull) but the main problem for
> that you have to maintain the direction of the pulling towards one side
> like z or x or y. As per my knowledge it is difficult in AMBER. But in NAMD
> you can try...
> I am still thinking pulling of the group of atoms in the same direction or
> pulling of only one atom or residue gives the same result or not. Because I
> think (may be I am wrong) pulling of the group of atoms in different
> direction is meaningless...
> I again suggest you can try with NAMD where you can maintain the direction
> of pulling with many atom...
>
> Thanking you...
>
>
> On Sat, 16 Jan 2021, 07:32 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>
>> 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
>>
>
--
Pinky Mazumder
PhD Student
University of Alabama
USA
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Received on Sat Jan 16 2021 - 10:30:01 PST
