Dear Xiaojiong,
The only way to use RAMD with AMBER is to compile AMBER8 with the RAMD
patch (available on Rebecca Wade's group homepage and on the AMBER home
page)...
The other option is to port the RAMD patch to newer versions of AMBER.
This might involve quite an amount of work. As I remember the
parallelization schemes have changed between AMBER8 and AMBER9 and that
was the reason it was difficult to port the RAMD patch.
Unless you want to port RAMD to newer AMBER versions, I would strongly
adise you to use the NAMD implementation.
AMBER8 is an old piece of software and it is likely you will have
problems compiling and running it on newer operating systems.
I don't see any reason why you cannot use NAMD for these simulations.
Best,
Vlad
On 18.03.2012 09:59, xiaojiong wrote:
> Dears,
> I want to use the RAMD method implemented in Amber8.Can you give me some advice what can I do?I know that NAMD implement RAMD,but I want use Amber!Thanks!
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Sun Mar 18 2012 - 03:00:03 PDT
