From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Mar 13 2011 - 12:49:51 CDT
Hello:
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
crash:
**********************************
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
(ARG, LYS).
Thanks for any suggestion about the trend of values to use in colvar.
francesco pietra
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