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\',
/
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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Received on Sun Dec 23 2007 - 06:07:32 PST
