From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 21 2015 - 05:31:57 CST
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
problem.
axel.
> 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).
>
> Jerome
>
> On 21 January 2015 at 08:54, 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.
>>
>> 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
>> ,...)
>>
>>
>> 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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