Re: NAMD-Lite

From: Axel Kohlmeyer (
Date: Tue Apr 15 2014 - 17:42:32 CDT

On Wed, Apr 16, 2014 at 12:22 AM, Hassan Kianinejad <> wrote:
> Dear NAMD users
> I have a question and I asked this many times, but no one replied.

asking the same question many times, doesn't make it a better
question. if you don't get an answer, then there is likely a reason:
- nobody knows the answer
- nobody cares
- people think that you should figure out the answer for yourself
- your question is ill posed

> I want to use NAMD benchmarks to run on NAMD-lite which is the sequential version; however the configuration files are different and they do not support each other.

they don't, because they are different entities. from the NAMD-lite home page:

NAMD-Lite is a rapid prototyping framework for developing new
simulation methods for biomolecules. It is a sequential, C language
code base consisting of modular parts that are easy to modify and
reuse. The intention is to separate the development of the method from
the additional complication due to parallel implementation, providing
a simpler way to test and validate new methods before bringing them
into NAMD.

that doesn't sound at all like it is a serial version of NAMD. more
like NAMD-lite is a code for people that know what they are doing
(which apparently doesn't apply as much to you). what is the reason,
you simply don't use NAMD as it is?

> I wondered if anyone could help me figure out a solution.

a solution to what? you are only asking half a question. how can you
expect a meaningful answer. i don't see a (NAMD) problem in need of
solving here.

> Thanks,
> Hassan Kianinejad
> Graduate Student

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

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