AMBER Archive (2007)

Subject: RE: AMBER: Steered MD

From: M kutty (mkutty_lists_at_hotmail.com)
Date: Sun Dec 23 2007 - 23:04:41 CST

Hello Mr. Dodson,
Thanks for the protocol.
I have found Steered MD protocol in Amber 8 manual page 145 (acroread page numbering). It uses RMSD wrt a reference structure and adds a kind of harmonic spring to the overall energy term to bias the traj to the ref structure or away from it (as far as I understood). At present I am trying to use that. Since I am new to amber I find your protocol quite out of my reach now but I'd experiment with your protocol too and will thank you again after I find its usefulness !!!!

- Vijay

> Date: Fri, 21 Dec 2007 10:00:58 -0600
> From: activesitedynamics_at_comcast.net
> To: amber_at_scripps.edu
> Subject: Re: AMBER: Steered MD
>
> M. L. Dodson wrote:
> > M kutty wrote:
> > > Hello All, If anyone has done/doing Steered MD / Targeted MD in
> > > AMBER, couldn't you please help me out with some tutorials, or
> > > protocols to follow ?
> > >
> > > Thank you in advance,
> > >
> > > -vijay
> >
> > Ok, this is the input file for a QMMM steered MD I ran:
> >
> > CBT-CAB, run steered QMMM, droping snapshots along the way
> > &cntrl
> > ntf = 2,
> > ntx = 5,
> > ntwv = 500,
> > jar = 1,
> > tempi = 300.0,
> > ntt = 1,
> > cut = 9.0,
> > tautp = 10.0,
> > irest = 1,
> > ntpr = 100,
> > iwrap = 1,
> > nstlim = 100000,
> > ifqnt = 1,
> > ntc = 2,
> > dt = 0.0005,
> > ntwx = 500,
> > /
> > &qmmm
> > qmcut = 9.0,
> > qmshake = 0,
> > iqmatoms = <this is a list of QM region atoms>,
> > qmtheory = 7,
> > writepdb = 0,
> > /
> > &wt type=\'DUMPFREQ\', istep1 = 500,
> > /
> > &wt type=\'END\',
> > /
>
> OK, due to the way I resurrected this file for this email enclosure,
> the \' stuff was inserted. Those should not be there.
> Sorry.
> Bud Dodson
>
> > DISANG=dist.RST
> > DUMPAVE=dist_vs_t
> > LISTIN=POUT
> > LISTOUT=POUT
> >
> >
> >
> >
> > In addition, you will need a dist.RST file (see DISANG variable
> > above) that defines the steered coordinate and any other
> > restraints:
> >
> > &rst iat=361,3384, r2=3.064234, rk2=5000., r2a=1.0,
> > /
> > &rst iat=2472,2477, r2=3.25, rk2=5000., r3=3.25, rk3=5000.,
> > /
> >
> > You probably do not want the QMMM stuff. The key variable in the
> > cntrl section is jar. jar=1 enables nmropt=1 (see page 160 of the
> > amber9 manual).
> >
> > Bud Dodson
> >
> > PS, before anyone points it out, the force constants for the
> > steered coordinate are very high as this run just dropped
> > snapshots along the coordinate. I save a "velocity trajectory"
> > and reconstruct restart files from frames of the coordinate and
> > velocity trajectories with a nab program.
> >
>
>
> --
> M. L. Dodson
> Business Email: activesitedynamics-at-comcast-dot-net
> Personal Email: mldodson-at-comcast-dot-net
> Phone: eight_three_two-56_three-386_one
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