VMD-L Mailing List

From: Nibedita Ray Chaudhuri (nivirc.143_at_gmail.com)
Date: Fri Nov 13 2020 - 00:54:16 CST

Thanks a lot for your response. I will try to troubleshoot the convergence
issue. Meanwhile, I will also try to address other possiblities and follow
up after that.

Nibedita

On Fri, Nov 13, 2020 at 10:24 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> So does the problem mainly arise from these modifications that are
> probably being reflected in the log files ?
>
>
> Indeed - one of the water molecules has impossible coordinates and at some
> point, clashes with an atom of your molecule, crashing the energy
> calculation. If it’s not converging you should investigate why - whether
> it’s too slow or some other cause. As much as we tried to automate tedious
> steps in FFTK, there’s no avoiding careful examination, e.g., of the
> individual water interaction calculations.
>
> Best,
> JC
>
> On Nov 12, 2020, at 11:36 PM, Nibedita Ray Chaudhuri <nivirc.143_at_gmail.com>
> wrote:
>
> I have used FFTK to generate the input gau files but I had to make slight
> modifications in the input format before submitting the gaussian jobs since
> they were not initially converging. For example:
> 1. Modified the coordinate input format from Z-matrix to the standard
> Redundant IC format of Gaussian calculation.
> 2. Used opt=calcfc to calculate the force constants once at the beginning
> of the calculation.
> The charge optimization step in FFTK requires the gaussian log files. So
> does the problem mainly arise from these modifications that are probably
> being reflected in the log files ?
>
> Nibedita
>
> On Fri, Nov 13, 2020 at 3:16 AM Gumbart, JC <gumbart_at_physics.gatech.edu>
> wrote:
>
>> Thanks for sharing your files. Something is wrong with your gaussian
>> input file, namely NG2-ACC-N2.gjf. It does not appear you used FFTK to
>> generate it.
>>
>> Best,
>> JC
>>
>> On Nov 12, 2020, at 12:48 AM, Gumbart, JC <gumbart_at_physics.gatech.edu>
>> wrote:
>>
>> Hi Nibedita,
>>
>> Did the tutorial work for you? Can you try to narrow down what is
>> different? If you can’t figure it out, you can send me files off list to
>> try to reproduce it.
>>
>> Best,
>> JC
>>
>> On Nov 6, 2020, at 6:22 AM, Nibedita Ray Chaudhuri <nivirc.143_at_gmail.com>
>> wrote:
>>
>> Hello,
>> I am trying to parameterize a small molecule following the fftk tutorial
>> using the fftk plugin of VMD version1.9.3, but I am getting the following
>> error in the Opt. Charges step:
>>
>> 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"
>> ......................................
>> ......................................
>>
>> I have been following the earlier threads but I am not sure what is the
>> specific problem in my case. I tried to do the same in the new version of
>> VMD 1.9.4a48 but this time it shows:
>>
>> ERROR) No molecules loaded.mol addfile operates on one molecule only
>> ERROR) No molecules loaded.mol addfile operates on one molecule only
>> while executing
>> "mol addfile $pdbPath waitfor all $cmpdMolID"
>> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 88)
>> 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)
>>
>> I checked my PSF file and apparently, everything seems fine. Is there any
>> way this problem can be resolved without having to edit the plugin code?
>>
>> I am pretty lost here. So, any suggestions will be highly appreciated.
>>
>> I am attaching the debugged log file. Please let me know if any more
>> information is needed
>>
>> Nibedita
>> <Charge-Opt.debug.log>
>>
>>
>>
>>
>