Re: Can I do ¡°accelerated molecular dynamics¡±in NAMD?

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Jul 25 2007 - 15:43:27 CDT

As far as I know, currently there is not any "official" implementation
of the accelerated MD in NAMD. However, you might contact some of the
people who have been working on this area and ask if they've done
something using NAMD. For instance, you could contact Donald Hamelberg
@ McCammon's group. He's been working basically with AMBER, but he
might have a code for NAMD. Michele Parrinello and co-workers are
developing the "metadynamics" technique, that can also be used to
explore rough energy landscapes (I've learned that some people have
successfully implemented metadynamics on NAMD, although only a few
collective variables are available in such implementation).

Sorry if the answer is limited, but that's the only thing I can think of :).

Good luck!
Michel

2007/7/25, Qiang Zhong <zqiang320_at_webmail.hzau.edu.cn>:
> Hi NAMD users:
> I have a protein transition cis/trans, because time scale is large than 100ns,
>
> I want to use ¡°accelerated molecular dynamics¡± to investigate the transition
> process, Could I do it in NAMD?
> Could somebody tell me how to do? Thank you very much!
>
>
>

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