AMBER Archive (2008)

Subject: AMBER: NMR optimization with group averages (IGR1 / IGR2)

From: Ryan Pavlovicz (pavlovicz.7_at_osu.edu)
Date: Fri Nov 14 2008 - 09:59:36 CST

Hi. I have been recently trying to implement some NMR optimization in
Amber9 where some restraints involve a group averaging. I have run previous
optimizations without group restraints and have had no problems, however
now, when IGR1 or IGR2 != 0, i am running into issues where i get the
following message:

vlimit exceeded for step 17; vmax = 20.1564
vlimit exceeded for step 26; vmax = 20.8039
vlimit exceeded for step 36; vmax = 20.3314
vlimit exceeded for step 56; vmax = 20.4082
vlimit exceeded for step 122; vmax = 20.8315
...
...

This violation seems to be linked to a slightly increased temperature I am
seeing -- temperatures closer to 308 K as opposed the to 300 +/- 1 K that I
was seeing in the stable NMR optimization trajectory without group
averaging. I have been running a series of optimizations where i slowly
release a restraint on the backbone atoms, while increasing the NMR
restraint force constants. The vlimit exceptions don't show up until after
several changes in the force constants have been made.

My input are as follows:

  &cntrl
   nstlim=50000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=500,
   temp0=300.0, ntt=1, tautp=2.0, taup=2.0,
   ntb=2, ntp=1,
   ntc=2, ntf=2,
   nrespa=1,
   nmropt = 1,
   ntr=1, restraint_wt=3.0, restraintmask=':1-326_at_CA,C,N,O',
  /
  &wt type='END'
  /
LISTOUT=POUT
DISANG=NMRrestraints_8.RST

-------------

NMRrestraints_8.RST sample:

 &rst
  ixpk= 0, nxpk= 0, iat= 903, -1, r1= 1.60, r2= 1.80, r3= 4.00, r4= 4.20,
igr1= 0, igr2=4238,4239,4240,
      rk2=8.0, rk3=8.0, ir6=0, ialtd=0,
 &end
 &rst
  ixpk= 0, nxpk= 0, iat= -1,3366, r1= 1.60, r2= 1.80, r3= 4.00, r4= 4.20,
igr1=1775,1776,1777, igr2= 0, &end
 &rst
  ixpk= 0, nxpk= 0, iat= 954, -1, r1= 1.60, r2= 1.80, r3= 5.50, r4= 5.70,
igr1= 0, igr2=4238,4239,4240, &end
 &rst
  ixpk= 0, nxpk= 0, iat= -1,3417, r1= 1.60, r2= 1.80, r3= 5.50, r4= 5.70,
igr1=1775,1776,1777, igr2= 0, &end
 &rst
  ixpk= 0, nxpk= 0, iat= -1,4236, r1= 1.60, r2= 1.80, r3= 5.50, r4= 5.70,
igr1= 963, 964, 965, igr2= 0, &end
 &rst
  ixpk= 0, nxpk= 0, iat=1773, -1, r1= 1.60, r2= 1.80, r3= 5.50, r4= 5.70,
igr1= 0, igr2=3426,3427,3428, &end
 &rst
  ixpk= 0, nxpk= 0, iat= -1, -1, r1= 1.60, r2= 1.80, r3= 3.70, r4= 3.90,
igr1= 963, 964, 965, igr2=4238,4239,4240, &end

Any suggestions on what is causing my problems?

Thanks,

ryan

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