From: Timothy Isgro (
Date: Tue Mar 07 2006 - 21:12:42 CST

Hi Vijay,
NAMD certainly can handle a simulation with DNA and protein. The
NAMD tutorial does not have any specific information on protein-DNA
interactions but it will certainly help you to get started on running
NAMD simulations. You can find it here:

To run your simulations, you will need topology and parameters for
DNA, which can be found at Alex MacKerell's website:

Also, the NAMD mailing list might be a good place to search or
address questions to should you run into problems with your simulations:

I hope this helps start you off,

i am new to namd. i have taken up molecular dynamics and simualtion
as my
final year project. I want to know the complexity that NAMD can handle.
i want to simmulate a dna- protein interaction with water as
enviornment. My
computaional facilities are a 8-node Beuwolf cluster.

is this feasible using NAMD?

i have tried a molecular dynamic simmualtion before but it was using
can you please suggest me the requirements and sources i can refer
for this

Thanking you
Vijay Santhosh Kumar
IV year Btech Bioinformatics
VIT , vellore.
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