Dear list,
I want to pull my protein using constant force. I have been told that this is doable using flat-well potential with NMR restraint. I tried to understand what the flat-well potential is and how to apply NMR restraint. I use the following control and RST file:
SMD at constant force
&cntrl
imin=0, irest=0, ntx=1,
ntt=3, gamma_ln=2.0, temp0=310.0, tautp=1.0,
ntc=2, ntf=2, ntb=2, ntp=1, pres0=1.0, taup=2.0, barostat=1
cut=10.0, iwrap=1, ig=-1,
ntpr=100, ntwr=100, ntwx=100
nstlim=150000000, dt=0.002,
ntr=1, restraintmask=".5,399,756", restraint_wt=1000
ioutfm=1, nmropt=1,
/
&wt type='DUMPFREQ', istep1=100 /
&wt type='END' /
DISANG=DISANG.f
DUMPAVE=dist_vs_t
DISANG=DISANG.f
&rst
iat=-1,-1,
iresid=0,ifvari=0,ir6=0,ifntyp=0,ialtd=0,
r3=83, r4=84.945,rk3=500,
igr1=5,399,756
igr2=386,743,1137
&end
I want to apply constant force between the centre of mass (COM) of 2 group of atoms. The initial distance between the COM of the 2 groups is 84.945. I want to stretch the protein at the COM of the 2 groups using constant force, which I think is equal to 2*rk3*(r4-r3) when the distance between the COM of the 2 groups is larger than r4. Under constant pulling force, the distance between the COM of the 2 groups should increase. However, from my dist_vs_t file, the distance between the COM of the 2 groups is decreasing from 84.945.
Is my understanding and my control and RST file correct?
Any help and guidance is appreciated.
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Received on Sun Jul 24 2016 - 18:00:02 PDT
