Thank you again.
I am trying to solve the problem as you said.
Sincerely,
Pinky
On Tue, Jan 12, 2021 at 1:44 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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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> >
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>
--
Pinky, Sharmi
AL,US
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Received on Tue Jan 12 2021 - 12:30:02 PST
