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
