Virtual Machine for Molecular Modeling

Key developers: Peter Pulay and Feng Wang

This is an NSF (Grant No. DMR- 1609650) funded project to create an integrated environment to learn and teach molecular modeling. It runs on virtually all platforms (Windows, Mac, Linux), and in most cases does not require software installation. The modeling software runs on a Virtual Machine, which isolates the modeling enviroment from the host operating system. This is a complete suite and it includes everything that is needed to explore molecular modeling of small and medium-sized molecular systems based on quantum or molecular mechanics.

The suite has two main components: a Graphical User Interface (GUI) for constructing molecules and displaying the computational results, and a computational engine which includes all major methods of molecular modeling. One part of the GUI, PQSMol, is used to construct and display molecular geometries, pre-optimizing their geometries, determining symmetry, and construct input for the higher level (quantum) calculations. The second part of the GUI, PQSView, displays results of the quantum calculations: optimized molecular geometries, optimization history, reaction paths, molecular orbitals, electron and spin densities, infrared and Raman spectra etc., NMR chemical shifts. The bundled computational engine is a serial version of Parallel Quantum Solutions (PQS) ab initio suite. It includes Hartree-Fock (HF), DFT, MP2, and Coupled Cluster energies for ground states, analytical first nuclear derivatives (forces or gradients) for HF, DFT and MP2, and second derivatives (Hessians, force constants) for HF and DFT, optimization of equilibrium geometries and transition states. Infrared, Raman and Vibrational Circular Dichroism spectra and NMR chemical shifts are also implemented for HF and DFT, and can be calculated numerically for other methods.

A tutorial for the GUI is included, and so is a User Guide for the PQS quantum chemistry program. A set of exercises (Understanding Chemistry through Computer Modeling) is provided to learn and practice molecular modeling. This booklet is being expanded.

As an example, a complete geometry optimization of cocaine (C17H21NO4) at the B3LYP/6‑31G(d) level (372 contracted atomic orbitals) takes about 2.7 hrs on a MacBook Air, running on a single core. This calculation was started with a geometry optimized with the Sybyl force field in PQSMol, then preoptimized at the 3-21G(d) level. Optimizing the more symmetrical and rigid azulene (C10H8, fused aromatic 7 and 5-rings) takes less than 2 minutes at the same level. We are working toward the release of the parallel version which will run 2-8 times faster on a typical PC or laptop.

The universality of our approach causes a minor inconvenience: the underlying operating system on all platforms is Linux which is basically a terminal-oriented operating system, and may be unfamiliar to users who grew up in the graphics-oriented world. Strictly speaking, one does not need to invoke Linux commands, as the GUI allows all operations to be carried out. Nevertheless, when something goes wrong, it is very useful to be able to invoke common Linux commands like cd (change directory), ls (list), rm (remove), cp (copy), mv (move or rename), top (list of running processes, also provides means to kill a process), etc. The Virtual machine contains a terminal program which behaves like a Linux terminal, and is similar to a Command box under Windows.

System Requirements:

A 64 bit CPU with at least 4G is memory is required. 10G of available drive space is required. You can run everything on a USB stick. However, it might run faster from a hard drive, either mechanical or SSD.

There are two installation methods: the Portable Virtualbox version and the Disk Image version. Once implemented, both run the same way for the user.

The Portable Virtualbox version requires no installation of additional software. It requires a 64 bit version of Windows 7, 8 or 10. The Disk Image version requires the installation of a hypervisor. It works under any operating system, Mac, Windows, or Linux. If you have a hypervisor installed on your windows machine. The disk image version gives more flexibility and possibly better performance, although we do not see significant differences.

Configuration of Computer for the Portable Virtual Box version.

For the Portable Virtual Box version to perform at the satisfactory speed, you will need to enable hardware virtualization support in the BIOS. This option could be referred to as Virtualization Technology, Intel VT, AMD-V, or similar languages depending on the motherboard and CPU. In many cases, probably most, this is already enabled on your PC. If you have trouble get into the BIOS on windows 10, please try this.

If you use the Portable Virtual Box, you need to disable the native Hyper-V support on windows 10. You do not have to worry about this on windows 10 Home edition since windows Hyper-V is only supported on higher version of windows, such professional or enterprise. The good news is that even on enterprise windows 10, the Hyper-V support is mostly likely not enabled by default. If you had a reason to intentionally enable Hyper-V support and know how to use it, you probably want to use the Image version under the windows 10 Hypervisor and not the Portable Virtual Box version.

If you want to use the Image Version rather than the Portable Version Box version, please install a hypervisor, such as Virtualbox or VMWare. Virtualbox is totally free. The free version of VMWare player is sufficient.

Downloading the ModelingVM

If you are running a later version of 64 bit windows (7,8,10), have no prior experience of Virtualization Technology, and have no other use of Virtualization Technology, it might be a good idea to try the Portable Virtual Box Version of the Modeling VM.

Download Portable Virtual Box version of PQS Modeling VM(1.5G)

If you are running Mac or Linux and have installed a hypervisor, such as Virtualbox, or running trouble with the Portable Virtualbox Version, please download the Disk Image version of the Modeling VM.

Download Disk Image version of PQS Modeling VM(1.4G)

Direct Link to Download Virtualbox

Using the Portable Virtual Box version of the Modeling VM.

Unzip the Portable Virtual Box version downloaded into a disk with at least 10G of free space.

Click on Portable-VirtualBox.exe. The executable may inform you a new version of Virtualbox is available. click ok but do not install the new version.

You should see the Oracle VM VirtualBox Manager.

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Click the Start botton on the tool bar.

The PQS_Comp_Chem virtual machine should start. Depending on the configuration on your computer, Portable Virtualbox may request elevated privileges to provide required services to the VM. Please grant the privileges if windows prompts for it.  Depending on the speed of your computer and the storage device, the boot process may take a few minutes.

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 You can see icons for pqsmol, pqsview, terminal, modeling tutorial, and the manuals. Double clicking on them starts the corresponding program. You have the choice to execute directly or in a terminal. It makes little difference which does one use but the direct mode is preferred. These programs can also be started from a terminal. For instance, the pqsmol molecule builder can be started by double clicking its icon, or double clicking the terminal icon, and type, at the prompt (pqsuser@PQSVM:)

pqsuser@PQSVM:cd ../PQS_JOBS

pqsuser@PQSVM:pqsmol

pqsmol is the graphical front end of PQS. For beginners, please start by reading the tutorial. pqsmol is virtually the same as the visualization program pqsview.

The terminal allows you to enter commands mentioned in the tutorial. If you have no Linux experience, the VM runs a light version of Ubuntu Linux, you may want to check out this Linux introduction, if you prefer a video introduction of Linux under a VM, please check out this. For instance, the pqs quantum chemistry code can be run from pqsmol or from a terminal. If you have an input file, say molecule.inp, you can run it from pqsmol by clicking on Calculation -> Browse, select and open the input file, then click again Calculation, click the input file name, and either edit it or submit it for calculation. To run from a terminal, go to the directory where the input is (see above), and type, at the prompt, pqs molecule.inp &

The ampersand makes the program run in the background, so that the terminal can be used again. One useful program removes old files associated with an input file. This carried out automatically, if wished, when running jobs from pqsmol but to clean up old files, issue the command (in the directory where the input is) tidy <jobname>, e.g., tidy molecule

You may have to adjust the screen resolution to accommodate all parts of the PQSMol/PQSView screen. To adjust the resolution, click on View (top of the screen), and the on Virtual Screen 1. It will show the current horizontal and vertical resolution as h x v. make sure that v is at least 800. The higher these numbers are, the smaller is the image. If the resolution is too low, parts of the PQSMol image, particularly the Restricted button (lower right corner of the pqsview window) are not visible and cannot be clicked on. On some MacIntosh models, the resolution can be adjusted only if you first switch to full screen mode. (You can switch back to terminal mode immediately.) To switch to full screen, push the F button while holding down the Home button. The Home button is different for different hardware but is shown at the right lower corner of the Oracle VM VirtualBoxx. It is often Right-Control (Windows) or Left-Command (Mac).

Using the Disk Image version of the Modeling VM.

To use the disk image version, please first install a hypervisor, such as virtualbox.

After you install and start Virtualbox, click on Machine->New

The name can be anything you want. However, please select Linux for Type and Ubuntu (64-bit) for Version.

Click on Next, pick a memory size. More memory will allow the VM to run faster. However, you probably do not want set the memory to more than 2G less than the total RAM on your computer.

When choosing the hard disk, please pick "Use an existing virtual hard disk file" and choose the downloaded PQS_Comp_Chem.vmdk.

Once you create the VM, please follow the instruction for the Portable VirtualBox version above, except you will be using your own Virtualbox installation.

Please email fengwang_antispam_uark.edu for broken links. (please replace _antispam_ with @.)