[gmx-users] Simulated annealing

[Mark Abraham]

Hi,

Simulated annealing for system preparation is a waste of time in my
opinion. Recommended simulation preparation protocols are on the Gromacs
website, and are all you need unless your starting conformation has serious
problems, and then simulated annealing may or may not help

Mark

On Wed, 31 May 2017 14:04 Venkat Raman <klvraman1993 at gmail.com> wrote:

> Hi all,
>        I am using Gromacs version 4.5.6 for peptide simulation. The
> structure of the peptide (16mer) was predicted from Pepfold3 server. I did
> Simulated annealing so that the side chains get properly oriented and the
> predicted structure will reach its global optimum so that the structure
> becomes more stable for production run. I have doubt in the mdp paramteres
> regarding position restraints and the annealing time and temperature. I
> tried with position restraints so that the backbone is restrained and the
> side chains are free to move. The annealing was pretty good. I did SA after
> NVT. I dont know to proceed further. How to finalize the mdp parameters
> like pressure couping and generate velocities for simulated annealing?
>
> Thanks in advance.
> K.L. Venkatraman
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>