VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Fri Sep 25 2015 - 16:18:52 CDT

*.top files, or topology files, are only used when generating the initial PSF/PDB pairs. Typically this is done prior to beginning the ffTK workflow; ffTK doesn't work with TOP files. However, if you intend to use topology files with PSFGen (or other structure preparation tools) to construct systems containing your newly parameterized molecule, then you should update the *.top file with the new charges.

Regards,
Christopher Mayne

On Sep 25, 2015, at 3:44 PM, Chitrak Gupta wrote:

Also, I realized that we are never updating the *.top file after optimizing the charges, which means that the *.top file has all atoms (except aliphatic H) with 0.000 charge. Is that ok?

On Fri, Sep 25, 2015 at 4:43 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu<mailto:chgupta_at_mix.wvu.edu>> wrote:
Hi Christopher,

Thanks for the explanation.

I am trying to optimize the dihedrals. The current FFTK version shows "QME" and "MME" along with the fitting (so a total of 3). Could you tell me what the difference between these are? Also, the QME and MME are varying at some points. is that normal?

I am attaching a pdf of my plot for your reference. Please note that it says "Orig" simply because I hit "Run Optimization" instead of "Run Refinement" during my last run by mistake. This is the result of a few rounds of optimization.

Regards,
Chitrak.

On Wed, Sep 23, 2015 at 10:56 AM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
Chitrak,

I have a question though. When I do the "scan torsion", there is a "Open Torsion Explorer" button that is not there in the video tutorial. Could you tell me what it is supposed to be used for? I was trying to use its "Analyze trajectory" button, but nothing seemed to happen.

The Torsion Explorer is a new tool in VMD 1.9.3 alpha builds that is designed to help map dihedral scans to the QM PES. At some point I was parameterizing a troublesome molecule and was unable to get the dihedrals to fit properly. It was difficult to identify which dihedral was causing problems. The Torsion Explorer shows the plot of the QM PES (or whatever scan log files are selected) and loads the scan trajectory into VMD. Each scan is color coded in the PES; while moving through the trajectory, a molecular representation identifying the dihedral that was scanned is shown using the appropriate color coding. The Analyze Trajectory button computes the current dihedral angle and the slope of the dihedral angle at every scan point. This will allow you to see which dihedrals are changing the most a particular part of the scan. Typically the dihedral that was being scanned should be changing the most. In highly coupled systems, however, this may not be the case, and it is often the source of problems when trying to fit the overall PES.

The other question I have is, from the video it isn't clear to me how to proceed on the optimization. For example, in the video, one of the dihedrals was duplicated. How do I know which one to duplicate? Also, when the video showed changing the periodicities to 3, is that a default setting (more like the 0.09 charge on aliphatic hydrogens), or was it specific to the molecule being discussed in the example?

The example molecule (pyrrolidine) in the screencasts contains sp3-hybridized carbons. If you map the dihedrals between the atoms using Newman projections, there are 3 local minima in the torsion (2 gauche and one anti); this type of torsional profile is best represented with a periodicity of 3.

A quick follow-up on that. Is the "periodicity" the same thing as the "multiplicity" in the manual (i.e. the n in the cos (n*phi - delta) term)? In that case, I am assuming n has to be adjusted for each one based on the molecule at hand, correct?

Multiplicity refers to the number of terms that are used to describe a single dihedral. Periodicity is the number of minima in the torsion (n).

Regards,
Christopher Mayne

On Sep 22, 2015, at 6:18 PM, Chitrak Gupta wrote:

A quick follow-up on that. Is the "periodicity" the same thing as the "multiplicity" in the manual (i.e. the n in the cos (n*phi - delta) term)? In that case, I am assuming n has to be adjusted for each one based on the molecule at hand, correct?

Chitrak.

On Tue, Sep 22, 2015 at 7:06 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu<mailto:chgupta_at_mix.wvu.edu>> wrote:
Hi Christopher,

Sorry for the late reply. I solved this issue, I basically had two NAMD executables by the same name which was creating confusion. I have it fixed now--_000_7F3F8154AB714C6684D9E9826CDF3697illinoisedu_--