Comments for Dr. Joaquin Barroso's Blog http://joaquinbarroso.com Scientific log of a computational chemist Thu, 31 May 2012 07:13:49 +0000 hourly 1 http://wordpress.com/ Comment on Rigid and Relaxed Potential Energy Surface Scans (PES Scan) in Gaussian 03 and Gaussian 09 by brad http://joaquinbarroso.com/2010/04/19/pesscan/#comment-2897 Thu, 31 May 2012 07:13:49 +0000 http://joaquinbarroso.wordpress.com/?p=136#comment-2897 First, great blog!

I would like to perform a relaxed PES scan in which two bond lengths change in concert. My problem is that if I request two variables to be scanned, g09 will calculate all permutations of possibilities but I only want the energies for when these two bonds are equal! Do you know how to request such a job? Thanks!

]]> Comment on Leave a question! by Moshe Nathan http://joaquinbarroso.com/questions/#comment-2894 Tue, 29 May 2012 22:04:46 +0000 http://joaquinbarroso.wordpress.com/?page_id=619#comment-2894 Dr Barroso,

We have been successfully running Gromacs (version4.5.3) simulations of tryptophan dipeptides for close to two years now. We build the dipeptide using PyMole and use the Gromacs command pdb2gmx in order to create at Gromacs topology file. We use the OPLS-AA force field with the suggested tip4p water model. For the first time we decided to run a tryptophan residue by itself. While the zwitterion simulation went without incident, the positively or negatively charged form of the residue repeatedly gave an error message.

The message we received was:

ERROR 1 [file topol.top, line 228]:
No default Ryckaert-Bell. types

ERROR 2 [file topol.top, line 229]:
No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 2 bonded neighbours molecule type ‘SOL’neighbours molecule type ‘SOL’

We are at a loss as to the meaning of this message as well as how to correct it. We narrowed down the error to the terminal carboxylic oxygens (line 228 – 229), but we do not understand what is wrong with them. In addition, it is the same terminal carboxylic oxygens as for the zwitterion species, in which the simulation ran well.
We suspect that the error is due to the fact we are running a single residue and not a dipeptide.
As a control, we tried running a simulation of single residue of tyrosine and it too produced a similar error message.
Any help or advice as to circumvent this issue would be appreciated.

Sincerely,

Dr. Azaria Eisenberg and Moshe Nathan
Brooklyn College – Dept. of Chemistry

ps

]]> Comment on Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09 by chemdz http://joaquinbarroso.com/2009/11/11/nbo/#comment-2893 Mon, 28 May 2012 18:54:14 +0000 http://joaquinbarroso.wordpress.com/?p=168#comment-2893 Hi
negative frequency means that there is a transition state

]]> Comment on Polarizable Continuum Model (PCM) in G03 by prema http://joaquinbarroso.com/2009/09/07/pcmg03/#comment-2892 Mon, 28 May 2012 07:03:58 +0000 http://joaquinbarroso.wordpress.com/?p=140#comment-2892 Dr. Borasso,
This blog is really helpful to get things clear and understand conceptually….thanks:)

]]> Comment on Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09 by praba http://joaquinbarroso.com/2009/11/11/nbo/#comment-2889 Mon, 28 May 2012 00:35:51 +0000 http://joaquinbarroso.wordpress.com/?p=168#comment-2889 i did’t understand

]]> Comment on Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09 by praba http://joaquinbarroso.com/2009/11/11/nbo/#comment-2888 Mon, 28 May 2012 00:33:51 +0000 http://joaquinbarroso.wordpress.com/?p=168#comment-2888 my input #p b3lyp/6-31G(d,p) opt freq=raman
got one nagative freq and 77 positive freq

]]> Comment on Analyzing Natural Bond Orbitals (NBO) results from Gaussian ’03 & ’09 by praba http://joaquinbarroso.com/2009/11/11/nbo/#comment-2887 Mon, 28 May 2012 00:30:52 +0000 http://joaquinbarroso.wordpress.com/?p=168#comment-2887 sir i run my compound using gaussian03,i got one negative frequency and 77 positive frequency.so how to modefy negative frequency.

]]> Comment on Rigid and Relaxed Potential Energy Surface Scans (PES Scan) in Gaussian 03 and Gaussian 09 by Mala Sainna http://joaquinbarroso.com/2010/04/19/pesscan/#comment-2880 Tue, 22 May 2012 01:13:20 +0000 http://joaquinbarroso.wordpress.com/?p=136#comment-2880 Hi joaq,

No words to thank you for your help, we so much appreciate your time and effort to help us.I am a research student working on gaussian03 and 09 for the first time. My aim is to model an iron crystal surface of around 24 Fe to examine the mechanism of synthetic gases on the surface; But the issue is i am struggling to calculate the SCF for months now but yet no success talk less of the optimisation and the rest. Please Please i will highly appreciate it if you can give me a helping hand on this.
Many thanks

Mala

]]> Comment on Leave a question! by Abdul http://joaquinbarroso.com/questions/#comment-2877 Mon, 21 May 2012 15:37:14 +0000 http://joaquinbarroso.wordpress.com/?page_id=619#comment-2877 Dear Prof. Joaquin,
I want to do IRC calculation in order to check if transition state is directly bound to reactant or product or there is any intermediate. I will be thankful if you could let me know the ways to calculate it. I tried but somehow it didnt work. Will be thankful if you could shed more information on this topic.
Thank you very much
Abdul

]]> Comment on Links by reza ghazfar http://joaquinbarroso.com/links/#comment-2874 Sun, 20 May 2012 17:48:08 +0000 http://joaquinbarroso.wordpress.com/?page_id=42#comment-2874 Dear Dr

Thank you so much for your precious advice.

Wish you all the best

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