Hello everyone,
I'm working on "Polymer translocation" and every time I search in internet, other researchers are talking about GROMACS. Is there a big problem with LAMMPS?
Is GROMACS so easier than LAMMPS?
[ I use PDB file in my work too and charmm2lammps.pl for making LAMMPS input]
Sincerely,
Mohammadreza Niknam Hamidabad
#LAMMPS #GROMACS
There's more to it than saying which program is easier, although it might indeed be slightly easier to get something up and running in GROMACS without getting cryptical errors. There is also no problem with LAMMPS. In fact, while LAMMPS has a bit of a learning curve, it is very flexible, which can be a great advantage if you want to do complicated things.
The main advantages of GROMACS would be the fact that it is very fast and that the format of the input data is a bit more common than the lammps data format.
Both programs you can learn without investing a great deal of time. Which one to choose probably depends on what kind of simulations you want to do now, but also perhaps in the future. Can the people around you help you with one of both programs? How big is your system and how important is speed?
There's more to it than saying which program is easier, although it might indeed be slightly easier to get something up and running in GROMACS without getting cryptical errors. There is also no problem with LAMMPS. In fact, while LAMMPS has a bit of a learning curve, it is very flexible, which can be a great advantage if you want to do complicated things.
The main advantages of GROMACS would be the fact that it is very fast and that the format of the input data is a bit more common than the lammps data format.
Both programs you can learn without investing a great deal of time. Which one to choose probably depends on what kind of simulations you want to do now, but also perhaps in the future. Can the people around you help you with one of both programs? How big is your system and how important is speed?
Dear Remco,
Thank you so much . Is it hard to learn GROMACS in a short time? ( I don't have any work experience with GROMACS)
Learning something new is always challenging for a bit, but there are excellent tutorials (I believe by Justin Lemkul) and also very good support. I would certainly not discourage you from becoming familiar with GROMACS early in your career. However, I would also not encourage you to move away from LAMMPS. So perhaps learn both? :P
It's polymer translocation. my system length is about 2 micrometers and in the best situation, with 1 ps timestep, is simulated about 20 ns. (the actual Polymer translocation is about 200-600 microseconds)
Nobody in my school is not familiar with MD software. I'm alone :D
I just need results I don't have problem with speed.
I would recommend also Justin Lemkul's tutorials for GROMACS. They are very helpful indeed and well explained. Also GROMACS' mailing list is very informative and sometimes there are very informative discussions.
Dear Mohamadreza,
As Remco pointed, GROMACS is so fast, because it uses united atom force fields. You said minimum time you need to simulate the polymer trans-location is an order of 200 microsecond, right? So, GROMACS helps you decrease the cost of simulation remarkably. Moreover, there is lots of routine, helpful and very user friendly tutorials to simulate various phenomena in GROMACS. I dont know about LAMMPS, but if there is no matter to use "united-atom force field" as GROMACS is faster than LAMMPS, I would recommend you to use GROMACS. Dont worry, it is not hard to learn how to work with it!!
That's not completely accurate. These simulation engines do not just use a particular forcefield. Nothing stops you from using a united atom forcefield in LAMMPS, or an all-atom forcefield in GROMACS. In fact, that's exactly what I do.
Comparing the same simulations system with the same forcefield, GROMAC is faster. If you start comparing different programs by applying different forcefields, that would be a skewed comparison of course.
- Badges
- Science topic