From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Sat Dec 09 2017 - 12:56:18 CST

David,

For the purposes of debugging/testing, I highly recommend making copies of the relevant files from the /noarch/fftk/ folder and editing those. If the changes are outside of the fftk_guiInterface.tcl file, then all you would have to do is source the edited file from the tkCon console to overwrite the existing procs. If the edits are in the fftk_guiInterface.tcl file, then you will need to close the fftk window, source fftk_guiInterface.tcl from the tkcon console, and then relaunch fftk (just type ‘fftk’ in the tkcon).

Once you are satisfied with the fixes, you can overwrite the file in /noarch/fftk folder to make the changes persistent. Oh, and let us know of fixes so that we can get things patched in the source code prior to the next VMD release (please, thank you).

Regards,
Christopher Mayne

> On Dec 9, 2017, at 5:33 AM, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
>
> Editing the code in the /noarch/tcl/fftk/ folder should work. But you will have to do
>
> package forget forcefieldtoolkit
> package require forcefieldtoolkit
>
> to get it to update. If you’re making changes to the GUI, you may end up needing to restart VMD altogether for changes to take effect.
>
> Regarding your specific problem, although you provided a lot of helpful information, I still can’t say for sure what’s causing it. Can you please send me your files (or a sufficient reduced set) so that I can reproduce it?
>
> Best,
> JC
>
>> On Dec 9, 2017, at 6:32 AM, David Fischermeier <david.fischermeier_at_gmail.com <mailto:david.fischermeier_at_gmail.com>> wrote:
>>
>> 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 <mailto: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
>>
>


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