From owner-chemistry@ccl.net Wed Dec  3 14:07:01 2025
From: "Grigoriy Zhurko reg_zhurko a chemcraftprog.com" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL: Using Chemcraft program for molecular dynamics calculations
Message-Id: <-55429-251203011723-24829-Uzea3R6gWJ8FYynUGAws5Q_-_server.ccl.net>
X-Original-From: Grigoriy Zhurko <reg_zhurko|,|chemcraftprog.com>
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Date: Wed, 3 Dec 2025 09:17:12 +0300
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Sent to CCL by: Grigoriy Zhurko [reg_zhurko---chemcraftprog.com]
Hello,
The latest version of my program Chemcraft has some features for working with molecular dynamics calculations, in particular it can visualize GROMACS files. Probably it is difficult for me to compete with VMD, since VMD is a freeware program (and Chemcraft is a commercial one), but I try to make some features which can be at least an addition to VMD for some tasks:
- Chemcraft can draw atoms with colors by the velocities of atoms or forces on them;
- While only .trr files contain velocities and forces, with Chemcraft you can read any file with trajectory (.xtc, .xyz, .irc) and compute the velocities as the difference between the coordinates of atoms in adjacent frames (or forces as well);
- Chemcraft can divide the system into residues and select individual residues; probably VMD can do this too, but maybe it does not provide the option to check or not to check H-bonds (so with Chemcraft you can select individual dimers, trimmers, etc.). Chemcraft has a “Fragment extractor” tool together with options for building a supercell, and maybe it provides more convenient ways for selecting a residue. Also, with Chemcraft, you can compute the size or a residue (the A, B, C parameters of a parallelepiped with the lowest volume fitting all atoms in the molecule);
 - Chemcraft can compute e.g. the numbers of dimers and trimers for each step in a trajectory, and show a graph;
 - Maybe Chemcraft provides more flexible options than VMD for choosing the parameters for identifying H-Bonds.
At this webpage you can see the description of Chemcraft features for molecular dynamics researchers with pictures:

https://chemcraftprog.com/gallermoldyn.html

So I have a question: can you suggest a forum in the Web, where molecular dynamics researchers are talking, and I will be able to tell them about Chemcraft?

Grigoriy Zhurko

https://chemcraftprog.com