Re: NAMD Non-features

From: Axel Kohlmeyer (
Date: Wed Jan 21 2015 - 05:24:41 CST

On Wed, Jan 21, 2015 at 2:54 AM, JAVAD NOROOZI
<> wrote:
> To dear developers,
> In a few month working with NAMD , i came across with some important
> Non-features which hinder working with NAMD.

strangely enough a ton of people *are* working with NAMD and quite
successfully and happily so, thus what you call "important" doesn't
matter to them. you have to rephrase this to "hinder *me* working with

> NAMD does not support...
> 1. non-equilbirum MD (multiple tcouple , multiple tcl forces, examples are
> measuring thermal conductivityand shear viscosity)
> 2. dummy or virtual sites (except for TIP4 water)
> 3. Rigid bond between two heavy atoms
> 4. Rigid bodies
> 5. Efficient solvation free energy methods( i.e , Expanded Ensemble , BAR
> ,...)

you sound like the guy with six children who bought himself a sports
car and now complains that it doesn't seat whole family. that is why
software has documentation and why smart people carefully study that
documentation and what other people do with a software before they
spend weeks of their time trying to make it work (unless they are
developers, of course, and have the intent of implementing the
features they are missing).

i understand your frustration, but you have to realize that this is
self-imposed and could have been easily avoided.


> Javad

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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