VMD-L Mailing List

From: LOISON CLAIRE (claire.loison_at_univ-lyon1.fr)
Date: Fri May 20 2016 - 04:29:14 CDT

Dear FFTK developpers,

The FFTK is a great help, thank you for your very nice job !

Here first small hints on what could be improved for the user in my opinion :

- in the torsion explorer and dihedral fitting :

adding small arrows to change the order of the QM log files.

When one loads several at the same time, they are in

order which are not always the best to investigate afterwards...

- in the dihedral results (energy curves).

Would it be possible to see the results of the

energy scan before any optimization (total MM energy from the input par) ?

Would it be possible to save energy curves into text files to compare

different approaches afterwards ?

Or alternatively : where are the files stored by FFTK during its working process ?

- would it be possible to add a new function, after the model is done (after the dihedral fitting),

 where one could compare the QM and MM energies of abritrary

conformations (taken for example out of a G09 log file), without optimizing ?

My idea behind this question is to test the model on conformations which where not used before during the optimization, or to see the impact of parameters which are not considered before, of scans which are not the previous dihedral scans. I think for example about NBFIX parameters. The idea would be similar to the dihedral optimization, but without the optimization procedure. It would also be great to have the option to visualize and store several energy data for different par files.

And now questions linked to my difficulties with an optimization of a small organic molecule based on CGFF?. I had the impression that my difficulty emerge because of intermolecular H-bonds, between several close alcools, a bit like in glycerol or sugars. Therefore, I have cut the molecule into pieces to get most parameters when this intermolecular H-bonds are not present. When I use these parameters for the molecule I want, most of the dihedral scans are well reproduced, but their are a few isolated points where the MM energies are several kcal/mol lower.

 As far as I understood, these problematic cases appear

in the presence of intermolecular hydrogen bonds

with relatively long O...HO distance (2.3Ang) , which

seem too favorable in the MM model (by several kcal/mol !?).

I tried to play with the charges, but I was not able to improve.

I also tried some NBFIX, but this did not improve either.

Do you have any advise or strategy for that ?

- During the MM energy calculation, are the MM configurations

forced to remain on the QM geometries or are they optimized

with the dihedral constrained ? If they are optimized, is it possible to investigate the

geometries of the MM dihedral scans to look for MM/QM discrepencies ?

Thank you for any help ! Best regards,

Claire

?