I want to study the crystallographic phase transitions of crystals with increasing temperature. Which freely available MD package should I choose, which has easily available tutorials/example-input-files for this kind of work?
$\begingroup$
$\endgroup$
8
-
1$\begingroup$ MD is only as accurate as the force-field used. Most freely available MD codes have freely available FF's for biomolecular simulations $\endgroup$– B. KellyFeb 15, 2022 at 23:25
-
1$\begingroup$ Did you choose something yet? What options have you considered? The two most popular MD programs here seem to be LAMMPS and GROMACS. Is that right @B.Kelly? $\endgroup$– Nike DattaniSep 2, 2022 at 21:48
-
$\begingroup$ comment only based on limited exposure: "which has easily available tutorials/example input files" certainly applies to LAMMPS! $\endgroup$– uhohSep 3, 2022 at 1:07
-
$\begingroup$ @uhoh I'm curious how you saw this question? It wasn't active for 6.5 months, so it wasn't bumped to the top. I commented on it (which doesn't bump the question to the top) and the next day you saw the question?! $\endgroup$– Nike DattaniSep 6, 2022 at 19:58
-
1$\begingroup$ @uhoh actually when a question is bumped by the community user, there is a trace, but you have to look at the timeline or edit history to see it. This only happens when a question has at least one answer though, so it's not what happened on this question :) By the way user49535, how is this problem going for you? Did you choose a software to use yet? $\endgroup$– Nike DattaniNov 1, 2022 at 18:57
|
Show 3 more comments
1 Answer
$\begingroup$
$\endgroup$
1
LAMMPS
Any popular MD software is likely to allow you to study phase transitions with increasing temperature. LAMMPS slightly beats GROMACS in terms of activity here on MMSE, since the lammps tag has 82 questions in total and 38 asked this year, whereas the gromacs tag comes in a close second with 69 questions in total and 36 asked this year. Our LAMMPS chat room is also a bit older than our Gromacs chat room and the LAMMPS one has more active users and more messages from users in it.
Here's some information about LAMMPS:
Advantages:
- Free, and open-source (GNU GPL license).
- Long history: First released in 1995 (4 years after Gromacs in 1991, although Gromacs was based on an earlier program called GROMOS from 1978).
- Under very active development: For many codes, the majority of the development was done years or decades ago, but the development of LAMMPS seems only to have grown, not waned. This is also true for Gromacs, but LAMMPS has 220 contributors on GitHub whereas Gromacs only has 81. I've even seen a LAMMPS simulation being done on a smartphone back in 2018, and I could see a plot that was changing in real-time as the calculation was being done!
- Since the very beginning (decades ago), it was designed to run in parallel (i.e. fast). In fact the "MP" in LAMMPS" stands for "massively parallel"! There's also support for GPUs.
Disadvantages:
- Basically all of the advantages listed above are also true of Gromacs (and Gromacs has been developed for longer, but LAMMPS has more developers currently, which is probably more important in the long-run).
- According to Steve Plimpton, a fator of 2x speed-up in GROMACS compared to LAMMPS is "not surprising" because GROMACS has pairwise interactions implemented in assembly code.
- It is primarily a classical MD code, so quantum effects are not the focus. QM/MM is possible, but would require using one of the interfaces.
answered Nov 1, 2022 at 19:38
-
$\begingroup$ I will add something to Nike's answer. Irrespective of the choice of MD software, you have to perform various other analyses (e.g. - Local structure analysis, g(r), etc), which may or may not be included in your MD tool. For this, you can write your own code, also there are several post-processing tools out there that can do the heavy work for you. OVITO or MDAnalysis are among some of the popular and frequently updated tools you can take a look into. $\endgroup$ Nov 2, 2022 at 17:00