From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Wed Jan 21 2015 - 09:35:27 CST
As Axel and Jerome have noted, it is impossible for one MD software to
support every method and force field that's out there.
I'd recommend Gromacs for (2) virtual sites, (3) rigid bonds between
heavy atoms, and (4) rigid bodies. You might note that faithful
implementations of MARTINI cholesterol, proteins, and polarizable
water require (3). I believe that the experimental MARTINI nucleic
acids require (2).
However, NAMD is open source, and you can make it do whatever you
want! For example, it can easily be modified to support polarizable
MARTINI water and other force fields (such recent gold and silver
models) with single-valence rigidly bonded particles. NAMD currently
uses a mass criterion to determine whether a particle is a "hydrogen
atom," for which a rigid bond is needed. 1.0 >= mass >= 3.5 is a
hydrogen atom. Search for "3.5" in Molecule.C and you can easily
change this criterion. I do this routinely.
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
On Wed, Jan 21, 2015 at 5:31 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Wed, Jan 21, 2015 at 5:38 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>> Dear Javad,
>> NAMD does not try to be everything to everyone. For points 2 to 4 in your
>> list, LAMMPS is probably the go-to package. A lot of your point 1 can
> LAMMPS doesn't do generic virtual sites either and rigid bonds between
> atoms are confined to isolated clusters.
> so it looks that javad will either have to write his own MD code or
> find a research project that doesn't require all of those features at
> the same time and learn to match the right MD code with the right
>> actually be scripted in NAMD. Not sure what you mean with "multiple Tcl
>> forces". One script can apply as many forces as you want. And you can do BAR
>> in NAMD (or rather by prostprocessing data from NAMD).
>> On 21 January 2015 at 08:54, JAVAD NOROOZI <noroozijavad_at_remove_yahoo.com>
>>> To dear developers,
>>> In a few month working with NAMD , i came across with some important
>>> Non-features which hinder 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
> 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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