struanr

Hello again, A minor correction to the link I gave it should be: https://mesmer-kinetics.github.io/mxg/ Sorry for any confusion. Regards, Struan

Hello, Firstly, sincere apologies for my very slow response. Regarding website https://www.mesmergui.cn/. I will try to find out what has happened to this site. In the meantime, you might try this website: https://mesmer-kinetics.github.io/mxg/dist/0.15 Regarding the acetyl example, and the lack of information on “me:deltaEDown” this will be set by MESMER to a default value and will appear in the output. For an example of this value being set please see the i-propyl example in the examples folder....

Hello, Apologies for my slow response. “In my system, I am modeling the association of reactants to a pre-reactive complex. I obtained temperature-dependent high-pressure-limit rate constants from POLYRATE (CVT/SCT calculations) and attempted to parameterize these rates in MESMER using the ILT formalism.” I am not sure I understand what you are doing, I think you mean that you have canonical rate coefficients from POLYRATE and wish to invert these to get microcanonical rate coefficients. “When fitting...

Hi Stella, Firstly, sincere apologies for my tardy response. Regarding your points: 1) Since you have an association reaction I would recommend ILT. There are variants of RRKM that can be used with barrierless reactions, such as FTST, but they typically require a lot more information about the potential energy surface. 2) I am always wary about negative activation energies. I know some authors are happy to cite them but when it comes to ILT such numbers can mean that you end up with negative or undefined...

Dear Stella, Thank-you for your reply and sorry for my slow response. It is good to read that you have been able to make progress. I did post a question on the OpenBabel discussion forum but have not yet received a response and suspect that this board is not being monitored. I will try to contact the team directly and let you know if I hear anything. With regards, Struan On Fri, 28 Nov 2025 at 05:42, Stella Lee stellal@users.sourceforge.net wrote: Hi Struan, Thank you for your reply, and my apologies...

Hi Stella, Thanks for getting in touch. I have downloaded OpenBabel 2.4.1 and run it as described in the MESMER notes and observed the same error as you did. I also observed that an output file was produced and that it gave a sensible rendering of the reaction scheme in FireFox. This file would almost certainly require some further adjustment to work properly but I think it has most of the data requried. In short I think that OpenBabel 2.4.1. is largely working but I agree the error message is a...

Dear Dr. Abbes, Thank-you for your message and for using MESMER. Unfortunately, the above command will not do what you wish, it would be nice if it could! The above command can only tell you where there are things missing, you must fill these items in yourself. I attach a revised pe.xml file with some suggestions of suitable content to add, but I suspect this will need a lot more work before it can be run. I hope this helps. Regards, Struan

Dear Dr. Szalay, Firstly, thank-you for using MESMER and sorry for my slow response. I have reproduced the problem and I agree the reaction between 7A and 7B is problematic though I also find problems with the reaction between 7C and 7D. Considering the reaction of 7A and 7B in isolation and inspecting the eigenvalues shows that the eigenvalue of smallest magnitude, which should be zero as defined by the the selected precision, is about 20 orders of magnitude larger than it should be and it is this...