[Tremolo-users] Tremolo- little guidance required

[Ralf Wildenhues]

Hello Nayyar,

* Nayyar Afaq wrote on Sat, May 03, 2008 at 09:36:14AM CEST:
> 
> Hope you would be fine. I have just googled up "Tremolo", and dont know much
> about the performance of it. Please, guide me about the given;
> 
>  1- Is Tremolo functionable in Windows? If not, please guide in which
> version of Linux it functions well?

It should work on both Windows and Linux, and all sorts of unices.  On
Windows, please install Cygwin and its FFTW and MPI packages prior to
building Tremolo.  Please report any build issues you encounter, so we
can fix them.

> 2- I want to get simulation study of mechanical properties of a Protein
> structure. Is Tremolo a good choice for it, i.e., Does Tremolo consider all
> the required interactions, like bonded, non-bonded, hydrogen bonding
> interactions, disulphide, salt bridge, etc.

With Tremolo, you have to list all bonded interactions explicitly,
esp. the hydrogen bonds, and disulphide and salt bridges.  Typically
this can be done easily with a preparatory script (we have one but it's
not fully general, so it may need to be adjusted for the input).  This
might require some small programming efforts.

Non-bonded interactions are handled as usual: excluded within the first
three bonded neighbors, and possibly scaled for the 1-4 neighbor.

> 3- Is Tremolo easy to understand and use. Infact, I have no skill of
> programming, and I prefer to work in user friendly graphical interface?

There is a graphical user interface that allows to adjust most settings,
but the atomic coordinates and connection data are so far read in via a
file only.  Also, there is unfortunately no extensive user manual yet.

Regards,
Ralf
-- 
Ralf Wildenhues      University of Bonn, Department of Numerical Simulation
                     Wegelerstrasse 6, 53115 Bonn, Germany
tel: +49 228 733178  mailto:wildenhues at ins.uni-bonn.de
fax: +49 228 737527  http://wissrech.ins.uni-bonn.de/people/wildenhues.html