VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue Jul 10 2012 - 08:57:56 CDT

Hello,

We've seen this error once before. It was due to a molecular size large enough that Gaussian stops printing the "Input Orientation" in the log file. The best method to fix this is to add "Geom=PrintInputOrient" to the Gaussian route section, which forces Gaussian to continue printing those coordinates.

There are potentially other issues that may cause this error, and I would suggest carefully checking your vdw parameters--the error is being thrown during the calculation of the vdw energy.

I would also like to point out that from the included log and debug log files, it appears that you only have a single oxygen atom in the optimization. There is no way to optimize the charge of a single atom, as it will just be assigned the charge necessary to achieve the final integer charge, taking into account any other atoms that were left out of the optimization (if any).

Chris

On Jul 10, 2012, at 3:30 AM, 肖富贵 wrote:

Hi all,
I am developing the force field of a small molecular, but in the Opt. Charges step i get an error: domain error: argument not in valid range
domain error: argument not in valid range
domain error: argument not in valid range
    while executing
"expr { sqrt($epsA * $epsH) * ( pow(($rminA+$rminH)/$dH1,12) - 2.0*pow(($rminA+$rminH)/$dH1,6) ) + sqrt($epsA * $epsH) * ( pow(($rminA+$rminH)/$dH2..."
    (procedure "::ForceFieldToolKit::ChargeOpt::computeIntE" line 46)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::computeIntE $i $j"
    (procedure "::ForceFieldToolKit::ChargeOpt::optCharges" line 77)
    invoked from within
"$function $p0list"
    (procedure "construct_initial_complex" line 13)
    invoked from within
"construct_initial_complex [lindex $args 0]"
    (procedure "::Optimize::Opt5::handle" line 89)
    invoked from within
"$opt initsimplex [lrange $chargeInit 0 end-1] " (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 340)
    invoked from within
"::ForceFieldToolKit::ChargeOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::coptRunOpt" line 55)
    invoked from within
"::ForceFieldToolKit::gui::coptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.chargeopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.chargeopt.runOpt state !pressed; .fftk_gui.hlf.nb.chargeopt.runOpt in..."
    (command bound to event)


and the debug file:
==========================================
 Charge Optimization GUI Debugging Output
==========================================
INPUT SECTION
psfPath: /home/xiao/CHARMM/FF/FOUR/F-1.psf
pdbPath: /home/xiao/CHARMM/FF/FOUR/F-Opt-Geometry.pdb
resName: UNK
parList:
 /home/xiao/CHARMM/FF/FOUR/BuildPar.par
 /home/xiao/CHARMM/cgenff2b7/par_all36_cgenff.prm
 /home/xiao/CHARMM/toppar/par_all27_na.prm
log file: ChargeOpt.log
-------------------------------------------
CHARGE CONSTRAINTS SECTION
chargeGroups: O28
chargeInit: -0.4510
chargeBounds: {-1.0 1.0}
chargeSum: -0.00
-------------------------------------------
QM TARGET DATA SECTION
baseLog: /home/xiao/CHARMM/FF/FOUR/UNK-sp.log
watLog: /home/xiao/CHARMM/FF/FOUR/wat-sp.log
logFileList:
 /home/xiao/CHARMM/log/UNK-ACC-O28.log
atomList: O28
indWeights: 1.0
-------------------------------------------
ADVANCED SETTINGS SECTIO! N
start: -0.4
end: 0.4
delta: 0.05
end: 0.4
offset: -0.2
scale: 1.16
tol: 0.005
dWeight: 1.0
dipoleWeight: 1.0
Optimization mode: downhill
Simulated Annealing Parameters: Temp. 25, Steps 20, Iterations 15
Override ReChargeFromPSF: 0
Override Charges:
debug: 1
==========================================
QME(water): -47665.46269478201
QME(cmpd): -1016446.108826478
scaled QMEn: -6.1217762373504225
QMDist (unshifted): 2.996476888656616
QM Standard Orientation Coordinates:
12.880990 0.514088 -0.811997
13.865997 -0.524906 -1.362997
14.396002 -1.455903 -0.282997
13.239007 -2.241910 0.317003
12.038002 -1.386917 0.648003
11.858994 -0.147918 0.115003
10.678989 0.678075 0.413003
9.393992 0.266068 0.264003
8.209987 1.065061 0.523003
6.984991 0.491054 0.307003
5.690987 1.084046 0.490003
4.533991 0.402040 0.239003
3.195988 0.916032 0.396003
2.142993 0.085026 0.095003
0.745991 0.377018 0.175003
-0.224004 -0.533988 -0.151997
-1.621005 -0.240996 -0.071997
-2.674000 -1.070002 -0.372997
-4.011004 -0.554010 -0.215997
-5.170000 -1.233017 -0.466997
-6.460003 -0.635024 -0.279997
-7.688000 -1.203031 -0.496997
-8.863004 -0.396038 -0.237997
-10.152002 -0.807046 -0.371997
-11.326007 0.013948 -0.065997
-11.! 466014 1.294947 -0.530997
-12.680019 2.090940 -0.222997
-12.768025 3.271939 -0.576997
-13.823015 1.404933 0.488003
-13.308008 0.338936 1.442003
-12.410002 -0.692059 0.750003
13.641984 1.608092 -0.045997
12.163986 1.159084 -2.005997
11.074006 -2.041923 1.603003
8.395979 2.477062 1.008003
3.024980 2.331031 0.878003
-2.505992 -2.486001 -0.856997
-7.883991 -2.613032 -0.984997
-10.467018 2.006953 -1.402997
-11.777997 -1.561055 1.846003
-13.235997 -1.591063 -0.184997
14.684994 -0.001902 -1.874997
13.352000 -1.128909 -2.123997
15.148006 -2.139899 -0.695997
14.895998 -0.878901 0.503003
12.927011 -3.034912 -0.380997
13.564010 -2.763908 1.226003
10.865984 1.710076 0.715003
9.221998 -0.748933 -0.097997
6.981996 -0.541946 -0.047997
5.630981 2.111046 0.841003
4.619997 -0.628960 -0.112997
2.395999 -0.921973 -0.245997
0.423985 1.363016 0.508003
0.098002 -1.519986 -0.485997
-1.871011 0.766002 0.270003!
-4.094009 0.476990 0.137003
-5.112993 -2.260016 -0.8179! 97
-6 .452009 0.397976 0.076003
-8.683010 0.617963 0.121003
-10.345996 -1.840047 -0.661997
-14.478012 0.962929 -0.274997
-14.411019 2.173930 1.001003
-14.142006 -0.179069 1.934003
-12.726011 0.825940 2.236003
14.360981 2.103096 -0.709997
14.185986 1.195095 0.808003
12.958979 2.376088 0.333003
12.901985 1.556088 -2.712997
11.512981 1.982080 -1.695997
11.546991 0.421080 -2.529997
11.627008 -2.486919 2.439003
10.530010 -2.860926 1.116003
10.341001 -1.339927 2.002003
8.965979 2.490065 1.944003
7.446976 2.984056 1.186003
8.959976 3.065065 0.276003
3.511976 3.033034 0.193003
3.487979 2.461033 1.863003
1.975978 2.618025 0.961003
-1.457991 -2.773995 -0.939997
-2.993988 -3.187004 -0.171997
-2.968992 -2.614004 -1.840997
-6.937989 -3.122027 -1.170997
-8.443988 -3.202036 -0.250997
-8.458991 -2.621036 -1.916997
-9.816014 1.301956 -1.921997
-11.001022 2.625949 -2.127997
-9.840022 2.687956 -0.816997
-12.! 567995 -1.980060 2.480003
-11.201992 -2.394052 1.433003
-11.110001 -0.966051 2.477003
-14.014995 -2.110068 0.384003
-12.603993 -2.351060 -0.654997
-13.712001 -1.015066 -0.982997
QM Dipole Vector: 2.6905 -4.1265 1.2192
QM Dipole Magnitude: 5.0747
Reference trajectory loaded: 12
Shift trajectories loaded: 13
234 elements added to ljPar array
95 elements added to atomInfo array
1615 elements added to atomDist


I am using the latest version of VMD 1.9.2 alpha 8
any suggestion is appreciated!