AMBER Archive (2002)

Subject: Re: restrain a residue as center of mass

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Nov 27 2002 - 15:34:00 CST

since targeted MD uses a restraint with a force constant, you cannot
get a zero deviation. you can reduce the fluctuations
by increasing the force constant, but this will increase the
frequency of the motion and thus require smaller timesteps.
If you want absolutely no internal motion, you'll
have to find another program that supports internal (not Cartesian)
constraints for subgroups of atoms.
Carlos

----- Original Message -----
From: "eric hu" <erichu_linux_at_yahoo.com>
To: "Carlos Simmerling" <carlos_at_csb.sunysb.edu>;
<amber_at_heimdal.compchem.ucsf.edu>
Sent: Wednesday, November 27, 2002 1:42 PM
Subject: Re: restrain a residue as center of mass

> Target md seems to satisfy what I want if I can use
> zero RMSD. I really do not want any internal motions.
> However, sander seems to stop running at a point. It
> gives the same result no matter if I assign the
> tgtrmsd or not.
>
> 4. RESULTS
> --------------------------------------------------------------------------
------
>
> ---------------------------------------------------
>
> eedmeth=4: Setting switch to one everywhere
>
> ---------------------------------------------------
> | Local SIZE OF NONBOND LIST = 462
> | TOTAL SIZE OF NONBOND LIST = 462
> SMALL DET 2.16840434497101D-019
> PROBLEM CALCULATING RMSDVALUE F
>
>
> Here is my input file.
>
> &cntrl
> igb = 0, ntb = 0, ntpr = 100, ntwx = 10,
> cut = 10.0,
> tempi = 300.0, temp0 = 300.0, ntt = 1, tautp = 0.5,
> imin = 0,
> nstlim = 1000, dt = 0.001,
> itgtmd=1
> &end
> Restrain the residue
> RES 1
> END
> END
>
> --- Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
> > if you're using amber version 7, you could use
> > targeted
> > MD to do this. Check the manual, it is the itgtmd=1
> > option in sander. What you want to do is to select
> > using the
> > GROUP input the residue to restrain, and then make
> > sure
> > to provide the reference coordinates for that
> > residue. This
> > will allow the residue to move as a group but will
> > restrain
> > it to be similar to the reference conformation. You
> > will want
> > to use a target rmsd value of something close to 0.
> > Post again if this isn't what you want or doesn't
> > work.
> > Carlos
> >
> > ----- Original Message -----
> > From: "eric hu" <erichu_linux_at_yahoo.com>
> > To: <amber_at_heimdal.compchem.ucsf.edu>
> > Sent: Tuesday, November 26, 2002 6:36 PM
> > Subject: restrain a residue as center of mass
> >
> >
> > > Hi, I want to freeze the internal motion of an
> > > unnatural residue which happens to have two
> > molecules.
> > > I still want the residue's center of mass to have
> > all
> > > the freedoms. I wonder if there is way to do this.
> > I
> > > have tried to constrain individual atoms or bond
> > > distances and they will either fix the atoms in
> > the
> > > space of there are still internal motions. Thanks
> > a
> > > lot.
> > >
> > > Regards,
> > > -Eric
> > >
> > > __________________________________________________
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>
>
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