Setting up values in distance colvar

From: Francesco Pietra (
Date: Sun Mar 13 2011 - 12:49:51 CDT

I am equilibrating a thoroughly minimized colvar-restrained protein in
a membrane. Heating alone (ts=1fs, only TIP3 hydrogens rigid), without
press equilibration, revealed problems with CLA-patched GLU. That is,
what was a respectful HE2-CLA distance during the minimization,
shortens too much below vdw and the procedure crashes. Of course I'll
try the common remedies, in particular ts<1fs and even slower heating
(it was starting 0.5K, frequency 25, reassign 5). However, having no
experience about, I wonder whether the values in colvar can also need
tuning for the case in point. What I used, just for the cause of the

colvar {
  name colvar9

  width 1.0

  lowerBoundary -10.0
  upperBoundary 10.0

  lowerWall -5.0
  upperWall 5.0

  lowerWallConstant 100.0
  upperWallconstant 100.0

  outputSystemForce yes

  distance {
    group1 {
      atomNumbers 20137 # CLA 421C(P3)
    group2 {
      atomNumbers 17866 # OE2 of GLU277C(P3)

harmonic {

  name CLA_harmonic

  colvars { colvar1 colvar2 colvar3 colvar4 colvar5
  colvar6 colvar7 colvar8 colvar9 }

  centers 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

  forceConstant 100.0

This means that I have restrained OE2-CLA.

No problems arose, in what I have done, with the other ligands of CLA

Thanks for any suggestion about the trend of values to use in colvar.

francesco pietra

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