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From: Pinky Mazumder <pmazumder67.gmail.com>

Date: Sat, 25 Jul 2020 23:16:28 -0500

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
*

*>>
*

*>
*

Date: Sat, 25 Jul 2020 23:16:28 -0500

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:

-- Pinky, Sharmi AL,US _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Jul 25 2020 - 21:30:03 PDT

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