Use remote desktop access for this like TeamViewer. By doing this you can access the desktop of remote machine and do simulation and all the work will be done by that remote machine. Make sure to have TeamViewer on both the systems.

I don’t think protein size or simulation time are anyway related with running remote machines.

if it’s a Linux machine that is going to perform the calculations, you should be able to establish a SSH connection with SSH command. If it is a windows you should do the same but with some extra steps.

And it is best to use nohup command or something similar to put the job in the background so closing ssh window or broken connection wouldn’t affect the running calculations.

You may transfer your files through sftp or scp commands. lastly, if you don’t have the root access to that remote computer make sure you are able to install gromacs through cmake options.

You can install cmake with no sudo command in the home directory, and then proceed to installation of gromacs or by connecting to the Remote Shell.

Tanusree Mookherjee Sir, you can use VPN also. Just check whether the institute, industry has VPN purchased or not. The strong network is required for VPN.

I want to do it without in cloud system as well. is that possible?

Tanusree Mookherjee

Cloud system/remote machines are different things.

Running simulations on a remote machine means that you are using a computer to connect to another one to launch simulations there. For example, you could have a workstation/computational cluster at your workplace, and connect to it from your home to check the simulations and launch new ones or download the results.

To launch GROMACS simulations on a remote machine, you need a remote machine with GROMACS distro on it, configured to be accessed remotely. For example, you could have a workstation with GROMACS2021 + Ubuntu, connected to the internet and ssh to it via another machine, e.g., your laptop or your cellphone.

Therefore, the answer to your 'how' is that you need a computer with GROMACS on it and to configure it to be accessed remotely. How to specifically achieve that, and what kind (~ simulation time length and dimension of your systems) of simulations you can run depend on a virtually infinite number of variables, first ones being by far the specifics of the remote machine you are using, i.e., number of cores, GPUs, HDDs etc.

Nicola Piasentin Thanks everyone for your precious time. I would like know to is it possible to run the program without the help of a remote machine? i.e like servers or using cloud computing? I am a student of biology and have very low knowledge of computational techniques.

Deat Tanusree Mookherjee

The program is just a program, like any other software it will in principle work on any machine where you install it, from your laptop to the largest computational cluster available (with some differences, clearly). The point is that these simulations tend to become heavy and complex quite easily, therefore your regular laptop will not be able to handle them and it becomes mandatory to use larger machines such as workstations, clusters etc.

If you are very new to the field, I suggest you not to take any definitive decision (as, for example, invest in a workstation) and do make yourself at least a bit used to the job you want to do. This set of tutorials from Dr Lemkul

http://www.mdtutorials.com/gmx/

has some introductory material on MD simulations with GROMACS and basic applications of very common and powerful computational techniques used everyday in MD to predict many quantities of interest. Some of the tutorials can be also run on a common laptop, although slowly. Consider that a decent general knowledge of MD and how it works is required, plus possibly basics on how to work on computer's terminals and so on.

If you want to install GROMACS and just play a bit with it, for example by running the first tutorial of the suite I linked in the latter, that is easily achievable by following the 'Quick and dirty installation' section of the official documentation

https://manual.gromacs.org/documentation/2021/install-guide/index.html

and if you are on Windows I highly suggest to install the Windows Subsystem for Linux (WSL) and then install there GROMACS

https://www.windowscentral.com/install-windows-subsystem-linux-windows-10

If you plan to run MD simulations, but have zero knowledge of what they are and how they work, then please start by making yourself comfortable with their basics, otherwise you won't be able to understand the results at all. There are many books out there on the subject, like 'Understanding molecular simulation' by Frenkel or 'Molecular Modelling' by Leach, alongside the GROMACS manual that enables you to go from the general concept to the specific algorithm implemented in the code.