Dear xiaojiong,
You can do the following:
1. Equilibrate your system with AMBER as you would do regularly.
2. Run an additional equilibration stage (NPT) in NAMD starting with the
AMBER equilibrated structure (NAMD can read AMBER topology and coordinates)
3. Do as much standard MD in NAMD as you wish
4. Start RAMD simulations
Please take a look at the NAMD documentation for specific input flags.
Some reading is required before you start ...
Please do some of the NAMD tutorials if you are not familiar with NAMD.
Please check this site as well: http://ambermd.org/namd/namd_amber.html
The RAMD is, I believe, quite well documented in NAMD. Just check the
NAMD user guide. If you have more specific questions, please address
them to me in private without the AMBER list ....
This issue does not concern AMBER users anymore.
Alternatively you can use the NAMD list.
Best,
Vlad
On 03/20/2012 08:12 AM, xiaojiong wrote:
> Dears,
> Can I use Amber11 to perform the MD to get the starting structure from the equilibration stage for the RAMD simulations in NAMD?What can I do?Because I am a new user,the work for me is difficult.On the other hand,I can't find tutorials for this simulation.So I don't know how to write the input file.Can you give me some help?The best thing is that you can give me an example!Thank you very much！
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, 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 Tue Mar 20 2012 - 01:30:03 PDT
