What is the initial value of that distance in the input coordinates? And
what is the energy at the first step? Try setting ntpr=1 and reduce nstlim
to see what is happening.
On Thu, May 15, 2025, 7:45 AM Sidharth E K via AMBER <amber.ambermd.org>
wrote:
>
>
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 15 2025 - 06:00:02 PDT
