[AMBER] Restraint ramp

From: Dhananjay <dhananjay.c.joshi.gmail.com>
Date: Sun, 18 Aug 2019 00:58:03 +0800

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

I want to increase the restraint on the positions of the proteins
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
  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,
  ntr=1, restraintmask=':1-306',
 &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.

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Received on Sat Aug 17 2019 - 10:00:01 PDT
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