From: JAVAD NOROOZI (noroozijavad_at_yahoo.com)
Date: Wed Jan 21 2015 - 15:24:43 CST
Axel,
I never meant to make you guys angry.I know that before solving a problem, first one need to find a suitabe tool or be smart enough to build his/her own tool. Non-features are usually is discovered after setting up a system , running the simulation and getting an error messages. Lammps has listed some of its Non-features in the begining of the manual, and you could perhaps do so. Finally i got what i wanted from NAMD, but this would help people to make a proper choice.
Javad
From: Axel Kohlmeyer <akohlmey_at_gmail.com>
To: NAMD list <namd-l_at_ks.uiuc.edu>; JAVAD NOROOZI <noroozijavad_at_yahoo.com>
Sent: Wednesday, 21 January 2015, 14:54:41
Subject: Re: namd-l: NAMD Non-features
On Wed, Jan 21, 2015 at 2:54 AM, JAVAD NOROOZI
<noroozijavad_at_remove_yahoo.com> 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".
> 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.
axel.
>
> Javad
>
>
>
>
>
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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