Hi,
I am a graduate student, pretty new to steered MD, and am interested in
using steered MD to study the effects of Gly-X mutations on the mechanical
properties of the triple helix. To perform steered MD, I want to keep the
COM of the three N-terminal Ca fixed (using a spring constant) and pull the
COM of the three C-terminal Ca atoms by linking them to a spring constant.
My current SMD script was created by referring to the Adaptive Steered MD
tutorial on the Amber website and is copied below. For reference, chain A
has residues 1-56, chain B 57-112, and chain C 113-168. I would appreciate
it if someone could guide me in implementing the previous calculation
method.
SMDrun script:
&cntrl
imin=0,irest=0,ntx=5,ntr=0,nmropt=0,iwrap=1,
ntb=1,ntp=0,
nstlim=25,dt=.002,
ntc=2,ntf=2,
ntt=1,temp0=300,tautp=10.0,
ntpr=10000,ntwx=10000,ntwr=100000,
cut=8.0, jar=1,
/
&wt type='DUMPFREQ', istep1=1000 /
&wt type='END' /
DISANG= dist.example.RST
DUMPAVE=dist.asmd.work.dat
LISTIN=POUT
LISTOUT=POUT
&end
Dist.example.RST file contains the following:
# Change distance between atoms 485 and 134 from 15 A to 20.0 A
&rst iat=168,2, r2=139.9, rk2 = 4000., r2a=149.9, /
I appreciate your help.
Sonal Gahlawat
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Received on Fri Apr 07 2023 - 18:00:02 PDT
