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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> > >
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Received on Tue Jan 12 2021 - 11:30:02 PST
