Re: Molecular Dynamics of Rigid Linear Molecules in NAMD.

From: Mike Makowski (
Date: Sun Sep 28 2014 - 03:03:10 CDT

​Hello Javad,

NAMD requires a parameter file designed to provide all the information of
your desired potential. To my knowledge, the accepted parameters must
conform to the syntax of CHARMM, AMBER or GROMACS parameter file formats.
That said, I'm assuming that you are attempting to model a CO2 TraPPE
​potential via syntax of one of these other force fields. If this is the
case than you will certainly be losing information from incorrect
assumptions. Can you be more specific about your approach to this problem
(e.g. how you're representing the TraPPE parameters)?


Michael Makowski
University of California, Irvine
Department of Chemistry,
Chemical and Material Physics,
Irvine, CA 92617
Cell: 267 588 9865
Office: 949 824 5776

On Sat, Sep 27, 2014 at 10:44 PM, Javad Noroozi <>

> CO2 is parametrized as fully rigid in TraPPE potential model,however, NAMD
> require spring constants for bond stretching and angle bending. Assigning
> very high values for these parameters require very small time step. Any
> idea how to solve this issue?
> Thanks in advance,

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