VMD-L Mailing List

From: David Fischermeier (david.fischermeier_at_gmail.com)
Date: Sat Dec 09 2017 - 05:32:50 CST

So apparently from what i can gather the problem arises from the VdW
parameters.

i tried using the blank paramater file generated early on:

===============
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
CB1I1 0.0 0.000000 0.000000 ! SET BY ANALOGY!!!
CB1I2 0.0 0.000000 0.000000 ! SET BY ANALOGY!!!
==== omitted parameters =====
NBSQ2 0.0 0.000000 0.000000 ! SET BY ANALOGY!!!
OBSQ2 0.0 0.000000 0.000000 ! SET BY ANALOGY!!!

END

==========

as well as my analogy-created prm file, which looks like this:

========================

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!DBT
CB1I1 0.0 -0.0990 1.8600 ! INDO/TRP CG2RC0
CB1I2 0.0 -0.0700 1.9924 ! INDO/TRP CG2R61
CB1I3 0.0 -0.0700 1.9924 ! INDO/TRP CG2R61
======= omitted parameters ====
NBSQ1 0.0 -0.0500 1.7000 0.0 -0.12 1.40 ! OG2D3
NBSQ2 0.0 -0.0500 1.7000 0.0 -0.12 1.40 ! OG2D3
OBSQ2 0.0 -0.0500 1.7000 0.0 -0.12 1.40 ! OG2D3
HBCAP 0.0 -0.0310 1.2500 ! alkene HGA4

END

=============================

both parameter files are capable of starting an MD simulation (although it
of course is nonsensical due to the lack of bond, angle etc. parameters),
which suggests, that the format should be alright.

Bonus question: is there an easy way to edit the plugin code, VMD is using,
to do some troubleshooting myself? If i edit the .tcl scripts in my program
folder nothing changes, so i assume that the plugins are already compiled
and pretty hard to change, but maybe smn has a good idea.

cheers David

On Fri, Dec 8, 2017 at 1:14 PM, David Fischermeier <
david.fischermeier_at_gmail.com> wrote:

> Hello fellow researchers,
>
> I have recently discoverd the FFTK plugin of VMD for the parametrization
> of smaller molecules (<50 Atoms).
>
> However I am encountering an issue while optimizing the charges in the
> Opt. Charges menu.
>
> *This is the Error Dialogue popping up:*
>
> =============================
> domain error: argument not in valid range
> domain error: argument not in valid range
> while executing
> "expr {$term / $sum}"
> (procedure "vecnorm" line 5)
> invoked from within
> "vecnorm $dipoleMMvec"
> (procedure "::ForceFieldToolKit::ChargeOpt::optCharges" line 141)
> invoked from within
> "$function $p0list"
> (procedure "construct_initial_complex" line 13)
> invoked from within
> "construct_initial_complex [lindex $args 0]"
> (procedure "::Optimize::Opt12::handle" line 89)
> invoked from within
> "$opt initsimplex [lrange $chargeInit 0 end-1] "
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 409)
> 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)
> =====================================
>
> *This is the gaussian command input I am using:*
>
> ------------------------------------------------------------
> -------------------
> # HF/6-31G* Opt=(Z-matrix,MaxCycles=100) Geom=PrintInputOrient
>
> which is as FFTK generates it.
> ------------------------------------------------------------
> -------------------
>
> *The debug file (ChargeOpt.debug.log)*
>
> ==========================================
> Charge Optimization GUI Debugging Output
> ==========================================
> INPUT SECTION
> psfPath: /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/DBT_gen.psf
> pdbPath: /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/DBT_gen.pdb
> resName: DBT
> parList:
> /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/par_SAB.LJ.prm
> /home/fischerd/SQA_GMX/FFTK/T3/par_all36_cgenff.prm
> log file: ChargeOpt.log
> -------------------------------------------
> CHARGE CONSTRAINTS SECTION
> chargeGroups: CBTC HBTC CSQ3 CSQ4 CSQ5 CSQ6 NSQ1 CSQ7 NSQ2 CSQ2 OSQ2 CSQ1
> CBBT HBBT C2I2 C2I1 {C2I3 C2I4} {H2I1 H2I2 H2I3 H2I4 H2I5 H2I6} N2I1 C2I5
> {H2I7 H2I8 H2I9} C1I6 C1I1 C1I5 H1I5 C1I2 H1I2 C1I4 H1I4 C1I3 H1I3 {HCA1
> HCA2}
> chargeInit: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
> 0.0000 0.0000 0.0000
> chargeBounds: {-1.0 1.0} {0.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0
> 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0}
> {-1.0 1.0} {0.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0} {0.0 1.0} {-1.0 1.0}
> {-1.0 1.0} {0.0 1.0} {-1.0 1.0} {-1.0 1.0} {-1.0 1.0} {0.0 1.0} {-1.0 1.0}
> {0.0 1.0} {-1.0 1.0} {0.0 1.0} {-1.0 1.0} {0.0 1.0} {0.0 1.0}
> chargeSum: 0.00
> -------------------------------------------
> QM TARGET DATA SECTION
> baseHFLog: /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/FDBT-sp-HF.out/
> opt.log
> baseMP2Log: /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/FDBT-sp-MP2.
> out/opt.log
> watLog: /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/Fwat-sp.out/opt.log
> logFileList:
> /home/fischerd/SQA_GMX/FFTK/T3/3-WATER/DBT/FDBT-DON-H1I4.
> out/rawDBT-DON-H1I4.log
> atomList: H1I4
> indWeights: 1.0
> -------------------------------------------
> ADVANCED SETTINGS SECTION
> 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): -630405.808215399
> scaled QMEn: -2.9972034683614037
> QMDist (unshifted): 2.4745562076568604
> QM Standard Orientation Coordinates:
> 4.600485 -2.070308 -0.120677
> 5.388393 -1.321594 -0.168832
> 3.321355 -1.505610 -0.049336
> 2.947888 -0.108060 -0.007492
> 3.659839 1.089510 0.040500
> 2.990879 2.345777 0.060656
> 2.422076 3.356064 0.071491
> 5.081949 1.102126 0.092816
> 6.239463 1.089845 0.140782
> 1.888535 -1.872438 -0.030550
> 1.257643 -2.916932 -0.022443
> 1.539962 -0.436898 -0.025950
> 0.444269 0.429907 -0.048275
> 0.742023 1.475584 -0.056724
> -0.930592 0.225870 -0.050105
> -1.752452 -1.063860 0.020898
> -1.529571 -1.934162 -1.229534
> -2.242304 -2.771391 -1.217818
> -1.702126 -1.356010 -2.149128
> -0.516820 -2.352011 -1.232886
> -1.456254 -1.852091 1.308119
> -2.170086 -2.684496 1.396357
> -0.447272 -2.277073 1.276256
> -1.568519 -1.214195 2.197538
> -1.781821 1.283022 -0.112566
> -1.401059 2.685083 -0.207654
> -0.497929 2.763056 -0.828928
> -2.200889 3.194235 -0.760777
> -1.164254 3.341056 1.151656
> -3.122968 0.870393 -0.038218
> -3.165229 -0.519625 0.038708
> -4.274571 1.646370 -0.037195
> -4.236796 2.735123 -0.083956
> -4.385428 -1.170436 0.110364
> -4.435246 -2.260380 0.168239
> -5.500067 0.980439 0.036278
> -6.423437 1.561942 0.040740
> -5.559323 -0.409867 0.108614
> -6.528964 -0.908200 0.166340
> 4.652856 -2.645492 -0.936918
> 4.746317 -2.639926 0.688640
> QM Dipole Vector: -10.8881 -1.2978 -0.5929
> QM Dipole Magnitude: 10.9812
>
> Reference trajectory loaded: 81
> Shift trajectories loaded: 82
>
> 241 elements added to ljPar array
> 41 elements added to atomInfo array
> 697 elements added to atomDist
>
> any help is gladly appreciated.
> regards David
>