RPMDRUN
RPMDRUN is a Volume,Temperature (V,T)-Replica Exchange Molecular Dynamics (VTREMD) simulation program. It can be used to perform simulations of an arbitrarily shaped extended ensemble of states in the V,T-plane, such as:
- Sampling along a line of isochoric states.
- Sampling along a line of isobaric states (which have to be identified in a preceeding independent simulation run).
- Sampling the entire V,T-plane using a grid of states.
- Multiplexed-Replica Exchange of one of the above.
RPMDRUN is based on the GROMACS 3.2.1 (not 3.3.X !) simulation package and is published under the conditions of the General Public license (GPL) .
-
The RPMDRUN sources:
rpmdrun.tgz
To compile the sources, a fully functional GROMACS 3.2.1 installation is required. -
The RPMDRUN mini-HOWTO:
rphowto.pdf
For details concerning the forcefield, the simulation setup, boundary conditions, treatment of long range electrostatics,... etc., I would like to refer to the excellent original GROMACS Manual. This little HOWTO just deals with aspects related to VTREMD simulations. -
Several Demo Applications:
rpmdrun_demo.tgz
REMD Simulations of several short peptides (16-21 residues) with explicit solvent (water). -
Helper applications:
rptools.tgz
The provided scripts and programs are necessary for running the demo applications. In order to be able to build the helper applications, install the MOSCITO package first.
Please note: I won't provide any support for these programs, nor answer any questions concerning them.
Dietmar Paschek 29th Sept. 2004