[AMBER] INFO Steered Molecular Dynamics

From: Francesca Di Matteo - francesca.dimatteo5.studio.unibo.it <francesca.dimatteo5.studio.unibo.it>
Date: Thu, 11 Nov 2021 15:12:04 +0000

To whom it may concern,

I'd like to perform Steered Molecular Dynamics at force constant (k).
I would like to perform steered on a RNA molecule and pull the two helices in different directions
that I want to be able to decide. How can I set these conditions in the input files, in particular, the exact pulling direction?
For reference I only have the examples given in the manual, which I copy below:

Sample pulling input
nstlim=1000, cut=99.0, igb=1, saltcon=0.1,
ntpr=100, ntwr=100000, ntt=3, gamma_ln=5.0,
ntx=5, irest=1, ig = 256251,
ntc=2, ntf=2, tol=0.000001,
dt=0.002, ntb=0, tempi=300., temp0=300.,
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /

The restraint file dist.RST in this example is:

# Change distance between atoms 485 and 134 from 15 A to 20.0 A
&rst iat=485,134, r2=15., rk2 = 5000., r2a=20.0, /

Kind Regards,

Francesca Di Matteo
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Received on Thu Nov 11 2021 - 07:30:02 PST
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