Re: Simulated annealing, in solvent or in vacuum?

From: Roshan Shrestha (roshanpra_at_gmail.com)
Date: Fri Sep 09 2016 - 03:17:37 CDT

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If you are trying to determine the secondary structure of proteins using
simulated annealing, then I suggest you to perform it in solution, however
I am not experienced on using this method in NAMD, though I have done it
using GROMACS. So, I hope other users can better help you with your query.
Thanks

On Fri, Sep 9, 2016 at 1:06 AM, faride badalkhani <farideh.khamseh_at_gmail.com
> wrote:

> Dear NAMD users,
>
> I need to perform simulated annealing simulations, but I do not know if I
> should perform it in vacuum or after adding solvent box! Could you give me
> some information about it, please?
>
> Regards,
> Farideh
>
>

-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal

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