From owner-chemistry@ccl.net Thu Jul 20 06:19:01 2023 From: "Grigoriy Zhurko reg_zhurko##chemcraftprog.com" To: CCL Subject: CCL: The Gromacs format and tools for MD analysis Message-Id: <-54972-230720061436-7604-btwG2ZYQ1cazFIAFesY5Bg^server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1250 Date: Thu, 20 Jul 2023 13:14:13 +0300 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko_._chemcraftprog.com] Hello, I want to improve visualization of MD/BOMD computations in my program Chemcraft. Firstly I have a question about the Gromacs .xtc format. I try to implement reading of these files in Chemcraft, and this is a binary format, not text as usual. Some information about this format it provided here: https://manual.gromacs.org/archive/5.0.4/online/xtc.html However from this description it is not fully clear for me, what means “int”, “float”, “float box”, “3dfcoord x”. Probably “int” means 4-byte integer, and what about “float” – is it 8-byte float or something else? How many bytes are in each “3dfcoord x”? How many elements are in “Float box” (probably 9)? The second question relates to MD/BOMD computations in general. The latest version of Chemcraft can perform manipulations with each step of a trajectory: for example, if you have a benzene ring, you can add plane by it, then compute the distance between this plane and a specified atom for each step, and show this distance on a graph “step N vs Value”. Can you suggest more features which will be useful for such research? Maybe e.g. computing the numbers of hydrogen bonds for each step, and showing these numbers on graph? Possibly the radial distribution function can be computed, how this is done? Or maybe I need to implement a script or even a programming language to make the user specify his own computations for each step? Grigoriy Zhurko https://chemcraftprog.com From owner-chemistry@ccl.net Thu Jul 20 13:02:00 2023 From: "SILPA ELIZABETH PETER peterpp1964 ~ gmail.com" To: CCL Subject: CCL: DFT calculations on Covalent Organic Frameworks Message-Id: <-54973-230720035319-29400-qgfM9TNz7d2FiHf7GKNZKQ[a]server.ccl.net> X-Original-From: "SILPA ELIZABETH PETER" Date: Thu, 20 Jul 2023 03:53:17 -0400 Sent to CCL by: "SILPA ELIZABETH PETER" [peterpp1964=gmail.com] Warm greetings to all, I am a research scholar from the Manipal Institute of Technology, India. I am working on Covalent organic frameworks (COFs) and their application in water treatment. One of my objectives is to calculate the binding energy of COF towards different pollutants. In our institute, we are using Schrodinger software. According to the literature review, in order to achieve this objective, I have to perform DFT calculations for optimizing the structures. i.e., optimizing COF, Pollutant, and COF + pollutant. Then calculate its binding energy. There is no option to create the periodic structure of COF in our software. Some papers have used truncated structure rather than porous cyclic structured COF for calculating COF. I am not familiar with these calculations, and I am facing some difficulties. even there is an option for adsorption studies in Schrodinger software. We used the truncated system and calculated the binding energy. We are not able to identify the interaction resulting in the binding. Regards Silpa. From owner-chemistry@ccl.net Thu Jul 20 15:58:00 2023 From: "zborowsk zborowsk : chemia.uj.edu.pl" To: CCL Subject: CCL: DFT calculations on Covalent Organic Frameworks Message-Id: <-54974-230720155055-22179-+aERVdFRz22jSjpso8EpKQ/a\server.ccl.net> X-Original-From: zborowsk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 20 Jul 2023 19:50:42 +0000 MIME-Version: 1.0 Sent to CCL by: zborowsk [zborowsk|-|chemia.uj.edu.pl] Hi It looks like calculations that can be made by any software. I do not think there must be any special option, for "adsorption studies", just perform calculations according to the mentioned scheme. I also think that cyclic structures can be calculated by any software. Where is the problem?? What additional option is necessary?? Of course, in some studies, simplified adsorbent structures may have been used for simplicity. It is, of course, impossible for us to try to identify the type of interactions without knowing the adsorbent and the compound adsorbing on it. Regards. W dniu 2023-07-20 07:53, SILPA ELIZABETH PETER peterpp1964 ~ gmail.com napisaÅ‚(a): > Sent to CCL by: "SILPA ELIZABETH PETER" [peterpp1964=gmail.com] > > Warm greetings to all, > > I am a research scholar from the Manipal Institute of Technology, > India. I am > working on Covalent organic frameworks (COFs) and their application > in water > treatment. > > One of my objectives is to calculate the binding energy of COF > towards > different pollutants. > > In our institute, we are using Schrodinger software. According to the > literature review, in order to achieve this objective, I have to > perform DFT > calculations for optimizing the structures. i.e., optimizing COF, > Pollutant, > and COF + pollutant. Then calculate its binding energy. > > There is no option to create the periodic structure of COF in our > software. > Some papers have used truncated structure rather than porous cyclic > structured COF for calculating COF. I am not familiar with these > calculations, and I am facing some difficulties. > > even there is an option for adsorption studies in Schrodinger > software. We > used the truncated system and calculated the binding energy. We are > not able > to identify the interaction resulting in the binding. > > Regards > Silpa. > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/-- Krzysztof K. Zborowski Faculty of Chemistry Jagiellonian University in Krakow 2 Gronostajowa Street 30-387 Krakow Poland email: zborowsk[A]chemia.uj.edu.pl