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Here, I explain how a patched GROMACS allows running of interactive simulations by implementing the interactive molecular dynamics (IMD) protocol. IMD allows monitoring of running simulations from a VMD client. In addition, the user can interact with the simulation by pulling on atoms, residues or fragments with a mouse or force-feedback devices.

Introduction

Interactive Molecular Dynamics (IMD) allows monitoring of and interaction with running simulations. The first NAMD - VMD implementation of IMD goes back to 2001 [1]. Recently, we implemented the IMD protocol into GROMACS v4.6 and the GROMACS master-branch. Features of our implementation are:

• Clean Interface: Only 4 hooks within the MD loop
• Correct PBC treatment, molecules are made whole as in input tpr
• IMD group can be set to interact with, transmit and display only a subset of atoms
• Negligible impact on performance (particularly when client is disconnected)
• Runs on Windows :-)

Flowchart of the GROMACS IMD implementation and the communication with a VMD client.

Installation

Currently, IMD for GROMAC is in review and most likely will be in the next major version. The github repository http://github.com/martinhoefling/gromacs contains two branches release-4-6-imd and master-imd, which both contain their respective non-imd patches plus imd-patch. Therefore, a IMD enabled gromacs version can be build from these branches as described briefly on http://www.gromacs.org/Developer_Zone/Git.

Simulation input preparation

The GROMACS implementation allows transmission and interaction with a part of the running simulation only, e.g. in cases where no water molecules should be transmitted or pulled. The group is specified via the IMD-group .mdp option. When IMD-group is empty, the IMD protocol is disabled and cannot be enabled via the switches in mdrun. To interact with the entire system, IMD-group has to be set to System, which is also the default for .tpr files created with an older version without IMD implementation. When using grompp, a .gro file to be used with VMD is written out ( -imd switch of grompp).

Starting the simulation

Communication between VMD and GROMACS is achieved via tcp-sockets and thus enables controlling an mdrun running locally or on a remote cluster. The port for the connection can be specified with the -imdport switch of mdrun, 8888 is the default. Every \(N\) steps, the client receives the applied forces from the VMD client and sends the new coordinates to the client. The initial frequency for communication with the client is set to the global communication frequency but can be altered using the -imdfreq switch. VMD also permits increasing or decreasing the communication frequency interactively. By default, the simulation starts and runs even if no IMD client is connected. This behavior is changed by the -imdwait switch of mdrun. After startup and whenever the client has disconnected, the integration stops until reconnection of the client. When the -imdterm switch is used, the simulation can be terminated pressing the stop button in VMD. This is disabled by default. Finally, to turn on interaction with the simulation (i.e. pulling from VMD) the -imdpull switch has to be used. Therefore, a simulation can only be monitored but not influenced from the VMD client when none of -imdwait, -imdterm or -imdpull are set. However, since the IMD protocol requires no authentication, it is not advisable to run simulations on a host directly reachable from an insecure environment. Secure shell forwarding of TCP can be used to connect to running simulations not directly reachable from the interacting host.

Connecting from VMD

In VMD, first the structure corresponding to the IMD group has to be loaded (File → New Molecule\ldots). Then the IMD connection window has to be used (Extensions → Simulation → IMD Connect (NAMD)). In the IMD connection window, hostname and port have to be specified and followed by pressing Connect. Detach Sim allows disconnecting without terminating the simulation, while Stop Sim ends the simulation on the next neighbor searching step (if allowed by -imdterm). The timestep transfer rate allows adjusting the communication frequency between simulation and IMD client. Setting the keep rate loads every Nth frame into VMD instead of discarding them when a new one is received. The displayed energies are in SI units in contrast to energies displayed from NAMD simulations.

References

[1] “A System for Interactive Molecular Dynamics Simulation” John E. Stone, Justin Gullingsrud, Klaus Schulten, Paul Grayson In 2001 ACM Symposium on Interactive 3D Graphics, John F. Hughes and Carlo H. Sequin, editors, pages 191-194, New York, 2001, ACM SIGGRAPH