Hi Carlos,
Thank you. The paper you given I have seen it. They pulled only head atom
of a chain, I need to pull multiple chains together towards a fixed atom.
Thanks again for your help.
Sincerely,
Sharmi
On Fri, Jan 15, 2021, 8:13 PM Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> You could try it and see, I know it is possible to use both a distance
> restraint and a Cartesian restraint at the same time.
>
> On Fri, Jan 15, 2021, 9:02 PM 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
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>>
>
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Received on Sat Jan 16 2021 - 14:00:03 PST
