Dear AMBER users,
I am relatively new to the use of restraints in the MD simulation.
Similar to temperature ramp to heat the system, I am trying to apply
restraint ramp to restraint positions of protein atoms only
(restraintmask=':1-306')
I want to increase the restraint on the positions of the proteins
gradually.
However, I am not sure how to apply the ramp on the proteins' position only
and solvent molecules unrestrained. I guess following will work.
equilibration rst
&cntrl
imin=0, irest=1, ntx=5,
nstlim=500000, dt=0.001,
ntc=2, ntf=2,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=500, ntwx=500, ntwr=5000,
ntt=3, gamma_ln=2.0,
temp0=298,
iwrap=1,
ntr=1, restraintmask=':1-306',
restraint_wt=1.0,
/
&wt TYPE='REST', istep1=0, istep2=250000,
value1=0.0, value2=1.0, /
&wt TYPE='REST', istep1=0, istep2=250000,
value1=1.0, value2=1.0, /
&wt TYPE='END' /
/
Does the above setting look good ?
I am not sure whether I should use restraint_wt=1.0.
Any input would be great help.
Thanking you in advance.
Best,
Joshi
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Received on Sat Aug 17 2019 - 10:00:01 PDT
