VMD-L Mailing List

From: surya narayanan chandrasekaran (sonofsunsurya_at_gmail.com)
Date: Thu May 30 2013 - 13:20:02 CDT

Hi,
Thank you for the reply. I have cleared the results window. Even I have
opened new vmd and tried but still the error retains. I was suspecting
about temp files like *opt.pdb or some files responsible for it. But I
looked at the terminal window it creates temp file. I have even cross
checked the log file the error occurred certainly in the simulated
annealing method. I have generated downhill charges but its exaggerated.

I have even doubt about the point charge correction factor? When I was
looking at some paper they spoke about the value 0.92 multiplication
factor. If you can give me any idea about it then it will be really
helpfull.

Thank you
Surya

On Thursday, May 30, 2013, Mayne, Christopher G wrote:

> I would suggest a fragment based approach to your validation.
>
> I'm pretty sure that I've determined the cause of your current error.
> This happens when running sequential optimizations without clearing the
> results box, changing the number of atoms that are included in the
> optimization from the preceding run. This is a bug; I will try to address
> it prior to the final 1.9.2 final release. In the meantime, if you change
> the number of atoms that are included in the optimization, first clear the
> results from any previous runs.
>
> The HF single point calculation is used to compute the interaction
> energy. The MP2 single point calculation is used to obtain the dipole
> moment.
>
> Regards,
> Christopher Mayne
>
>
>
>
> On May 30, 2013, at 6:11 AM, surya narayanan chandrasekaran wrote:
>
> Hi,
> There are enough literature for the system containing complete FF
> parameter. but our idea is to validate the FF for a specific purpose.
> Anyway i am now doing step by step approach. So I overcome previous error.
> But these is the new error:
>
> expected floating-point number but got ""
> expected floating-point number but got ""
> while executing
> "format %1.3f [lindex $finalCharges $i]"
> (procedure "::ForceFieldToolKit::ChargeOpt::optimize" line 439)
> 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 what it shows in terminal window.
> 90: -0.4164819391643594 -0.057477495153048785 0.04425565463821317
> -0.04191889719449131 -0.03481122763731818 -0.08942319851969328
> 0.04624171937672228 -0.1037705831593676 -0.014231337054360645
> -0.0057994098986916525 0.03862315687543251 0.12966829397588905
> 0.11067876264771703 0.027788216398095696 0.040788325942648355
> -0.015899829304677787 0.12501753558669915 -0.03544481078109548
> 0.08173920850142705 0.024192034588308806 -0.12295625392651034
> -0.12155047959722978 0.05367113097357905 -0.09597356868730267
> -0.020710520912424358 0.023326016393429752 -0.11162853863295871
> -0.007998571794961435 -0.051965910192716125 -0.12441090312713943
> 0.009197343605752398 0.06369351347099475 0.024741817301706385
> 0.13678531780791645 0.11745584123024622 0.10200486328480991
> -0.014086643959677996 -0.0006409063310558981 -0.10869521817879997
> -0.09276830393544586 0.0021942174951089964 -0.005008105141057144
> -0.20451319869279386 0.0418878010463012 -0.09787333093664699
> 0.056488065820808946 --> 920155169687.4338
> 91: -0.23815028187034218 -0.06525103392227471 -0.028171832141816337
> 0.04382305191973589 0.0027100264636047595 -0.029757812169598122
> -0.06117955141692656 0.01847534503385144 0.03870201348521461
> -0.012656532493677018 0.04429190563355304 -0.005814581663292849
> -0.003565664460958096 0.022831528883827088 -0.03189996406198106
> 0.03589885960661436 0.04494775796972928 0.07336468402161539
> 0.039455852232268246 -0.09782686370859789 -0.033467011704375285
> -0.007640869309604292 -0.06341002503057755 -0.05214537453043942
> -0.013774323263891821 -0.031170266091422837 -0.07877024630734503
> 0.022765472573900415 -0.011540892646115849 -0.045763900882304503
> -0.019793397545142602 -0.008902055179125186 0.009253131572992993
> 0.023548753794983387 0.02269153257719715 0.0024714908783821554
> 0.030113435215437967 -0.010926915334122097 0.029260463971165617
> 0.0017617155754303913 -0.03617586047344796 -0.0031835879545550026
> -0.1495432647529804 0.0542117078402133 -0.030551485775961323
> -0.02307231596308209 --> 920176214587.2339
> Simulated annealing:
> Initial temperature T0=25.0
> Number of T cycles Tsteps=20
> Simulated annealing step 0: T=25.0
> Already converged after T=25.0
> Simulated annealing step 1: T=0
> Simulated annealing converged.
>
> I tried in two ways still getting the same error?
> 1)What i did is calculated charges without hydrogen atoms but including
> charge file for hydrogen interacting water molecule same error comes.
> 2) Removing hydrogen interaction water molecule charge file and run the
> simulation. same error.
>
> once i tried the complete system too but i am getting the same error.
>
> I think its a minor mistake some where. if you can help then it will be
> great full.
> here are the list of files i loaded you can recreate it from my previous
> dropbox link
> BCL-ACC-C1A.log BCL-ACC-C4D.log BCL-ACC-ND.log BCL-DON-C2D.log
> BCL-DON-CHB.log BCL-DON-HAA2.log BCL-DON-HBD.log BCL-DON-HMC3.log
> BCL-ACC-C1B.log BCL-ACC-CAD.log BCL-ACC-O1A.log BCL-DON-C3B.log
> BCL-DON-CHC.log BCL-DON-HAC1.log BCL-DON-HCH.log BCL-ACC-C1C.log
> BCL-ACC-CGA.log BCL-ACC-O1D.log BCL-DON-C3D.log BCL-DON-CHD.log
> BCL-ACC-C1D.log BCL-ACC-CGD.log BCL-ACC-O2A.log BCL-DON-C4A.log
> BCL-ACC-C2B.log BCL-ACC-CHA.log BCL-ACC-O2D.log BCL-DON-C4B.log
> BCL-ACC-C2D.log BCL-ACC-CHB.log BCL-ACC-OBD.log BCL-DON-C4C.log
> BCL-ACC-C3B.log BCL-ACC-CHC.log BCL-DON-C1A.log BCL-DON-C4D.log
> BCL-ACC-C3D.log BCL-ACC-CHD.log BCL-DON-C1B.log BCL-DON-CAD.log
> BCL-DON-O45.log BCL-ACC-C4A.log BCL-ACC-NA.log BCL-DON-C1C.log
> BCL-DON-CGA.log BCL-ACC-C4B.log BCL-ACC-NB.log BCL-DON-C1D.log
> BCL-DON-CGD.log
>
> 

-- 
Suryanarayanan C
M.S Chemist
+94-01794019116