Look at the section titled "Steered Molecular Dynamics (SMD) and the
Jarzynski Relationship" in the Amber manual and comapre your input with
the one listed there.
I copy it here.
Sample pulling input
&cntrl
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.,
jar=1,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
So, to start, there is no need to set nmropt=1. Using just jar=1 is enough
More important, the dist.RST for the above run 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, /
and your is:
&rst
iat=6160,2493,
r1=0.0, r2=5.1, r3=5.1, r4=50.0,
rk2=0.0, rk3=10.0, /
Compare them carefully and check the manual for advice, but basically,
for SMD to work, you MUST have a value of r2=14.1 and r2a=5.1
and a value of rk2 > 0, otherwise you are not really applying SMD.
Please let me know if this is clear/unclear and if I can help more.
Adrian
On 5/15/25 7:44 AM, Sidharth E K via AMBER wrote:
> [External Email]
>
> Hello,
>
> I am currently trying to perform steered MD using amber so as to push a
> RNA micro helix to a protein's pocket with known binding site (Pushing
> from a distance of 14.1 Å to 5.1 Å). The steered MD using .RST file is
> tried so far but I am unable to change the CV. The inputs are attached
> here with
>
> For SMD:
>
> &cntrl
> imin=0,
> irest=1,
> ntx=5,
> nstlim=50000000,
> dt=0.002,
> ntc=2, ntf=2,
> cut=8.0,
> ntb=2,
> ntp=1, taup=2.0,
> ntpr=1000,
> ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> jar=1,
> nmropt=1,
> /
> &wt type='DUMPFREQ', istep1=1000 /
> &wt type='END' /
>
> DISANG=smd1.RST
> DUMPAVE=force_datac32.dat
>
> For .RST :
>
> &rst
> iat=6160,2493,
> r1=0.0, r2=5.1, r3=5.1, r4=50.0,
> rk2=0.0, rk3=10.0,
> /
>
> This does not worked well for the system and increasing restraints
> destabilizing the system.
>
> Can anyone tell me the about the possibility of this .RST based method?
>
> To change the CV the I read that patching of PLUMED with AMBER is
> needed. If anyone did the same it will be much helpful to get the
> insights about patching and further processing with PLUMED-AMBER SMD.
>
> Regards,
>
> Sidharth.E.K.
>
> PhD Scholar
>
> IIT Bombay
>
> 24d0242.iitb.ac.in
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 15 2025 - 09:30:02 PDT
