AMBER Archive (2007)

Subject: Re: AMBER: Steered MD

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Fri Dec 21 2007 - 10:00:58 CST

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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