From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Apr 01 2009 - 03:24:52 CDT

Dear NAMD users,

Since I got some questions about the method developed in our group
(Random Acceleration Molecular Dynamics - RAMD) to investigate ligand
exit pathways from buried active sites in proteins I thought of sharing
with you the latest developments regarding the implementation of RAMD as
a tcl module for NAMD.

The method was implemented in AMBER8 before I joined the group. Porting
it to AMBER9 and later AMBER10 is rather difficult (especially since I
don't know fortran and parallel programming).

So, whenever I was asked about RAMD I had to tell people to compile an
old version of AMBER if they want to use it. Then I thought it would be
very straight-forward to implement it in NAMD as a tcl module. I started
working with the ABF module, and I got inspired by it so I started
building a similar module for RAMD.

In the meantime in a recent paper (Biophys J. 2008 Nov 1;95(9):4193-204.
Epub 2008 Aug 1) Vashisth H et al, report a tcl script for running RAMD
in NAMD (available as supplementary material). Although the script does
what RAMD is meant to do, the runs cannot be controlled via the NAMD
configuration file (you always need to modify the script if you want to
run different trajectories). This script does not perform combined
RAMD-MD as our AMBER8 implementation does. The runs with this script are
not reproducible even on single CPUs simply because the script uses the
rand function in tcl without initializing it by srand. Also, the output
is not formatted in a nice way to extract the relevant information for
assessing the trajectory.

A while ago I have finished a version of my RAMD module for NAMD. The
runs are fully controlled from the NAMD configuration file. The module
compares to the Vashisth script but its more complex and can do almost
everything that our AMBER8 implementation can do. There is still one
difference though: the input is a force constant while in AMBER is an
acceleration. Because of this the results are not yet fully comparable.
The module is not bullet-proof tested yet but if people are interested
in testing and using it, I'd be happy to share it and if it proves
useful and easy-to-use I will ask the NAMD developers what to do to
include it in NAMD (if that's possible)... I also started working on a
new version that should be identical to the AMBER8 implementation (not
ready yet though).

As I said, for building this module, I inspired myself from the
structure of the ABF module, so I am grateful to Jerome, Chris and all
others that contributed to the ABF module. My RAMD module was also
compared against the Vashisth H et al. script, and I greatly acknowledge
their work which gave me the motivation to continue working on the module.

Feel free to contact me for the scripts in case you wish to test them.
As I said, they still need careful testing before using them for
production runs. For testing, I recommend careful comparison with Vanish
script (if you add an srand statement in that script and use the same
parameters - including random number seed - ) and run on 1 CPU you
should get the same results. If usage feed-back is good, I will put an
effort to include a standard test .

Best wishes

Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
EML Research gGmbH
Amtgericht Mannheim / HRB 337446
Managing Partner: Dr. h.c. Klaus Tschira
Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter

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