Yes you can add more restraints to the list if you want.
Keep in mind that these are just tools and you need to decide how to apply
them to solve the problems that you are studying.
We can help with the tools, but your questions are more about simulation
design.
You are probably the one that knows your system and your goals best, so you
need to decide how to use the tools to accomplish your goals.
On Tue, Jan 12, 2021 at 2:30 PM Pinky Mazumder <pmazumder67.gmail.com>
wrote:
> Thank you so much.
>
> I have another question, if I need to move top layers(group atoms) towards
> a fixed (group) atom, and bottom layers towards another fixed atom. Both
> top and bottom will move in opposite directions, in that way, how may I use
> these scripts?
>
> Do I need to use two scripts? or, I can merge all inputs in one file.
>
> I hope you understand my problem.
>
> Thanks in advance.
>
> Sincerely,
> Pinky
>
> On Tue, Jan 12, 2021 at 1:26 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > I am not sure if there are tutorials, you can check the Amber page.
> > here is a sample input with COM distance restraint.
> > this one changes the target distance with time. Look in the manual if you
> > need more details on these flags.
> >
> > MD with varying COM distance restraint
> > &cntrl
> > imin = 0, nstlim = 1000000, dt = 0.002,
> > irest = 1, ntx = 5, ig = -1, temp0 = 300.0,
> > ntc = 2, ntf = 2, tol = 0.00001,
> > ntwx = 500, ntwe = 0, ntwr = 500, ntpr = 500,
> > cut = 10.0, iwrap = 0,
> > ntt =3, gamma_ln=1.0, ntb = 1,
> > nscm = 1000, ioutfm=1, ntxo=2,
> > nmropt=1,
> > /
> > &wt
> > type='END',
> > &end
> > &rst
> > iat=-1,-1,
> > igr1=701,717,736,750,762,781,800,811,
> > igr2=920,930,945,961,978,997,1009,1033,
> > ifvari=1, nstep1=0, nstep2=1000000,
> > r1=5.0, r2=10.0, r3=10.0, r4=100.0, rk2=10., rk3=10.0,
> > r1a=5.0, r2a=25.0, r3a=25.0, r4a=100.0, rk2a=10., rk3a=10.0,
> > &end
> > &rst
> > iat=0,
> > &end
> >
> > On Tue, Jan 12, 2021 at 11:39 AM Pinky Mazumder <pmazumder67.gmail.com>
> > wrote:
> >
> > > Hi Carlos,
> > >
> > > Thank you.
> > >
> > > Should I use the igr command? Is there any tutorial in AMBER where
> they
> > > used the com distance?
> > >
> > > If there is, please let me know. That would be great for me to easily
> > > understand.
> > >
> > > Thank you very much.
> > >
> > > Sincerely,
> > > Pinky
> > >
> > >
> > > On Mon, Jan 11, 2021, 12:43 PM Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > one option is to use center of mass distance restraints. See section
> > 27.1
> > > > of the Amber 20 manual.
> > > >
> > > > On Mon, Jan 11, 2021 at 1:35 PM Pinky Mazumder <
> pmazumder67.gmail.com>
> > > > wrote:
> > > >
> > > > > Dear AMBER Users,
> > > > >
> > > > > Do you know how to pull a group of atoms together?
> > > > >
> > > > > Thank you.
> > > > >
> > > > > Sincerely,
> > > > > Pinky
> > > > >
> > > > > --
> > > > > Pinky, Sharmi
> > > > > AL,US
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>
>
> --
> Pinky, Sharmi
> AL,US
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Received on Tue Jan 12 2021 - 12:00:02 PST
