[gmx-users] How to dynamically change the "pull-coord1-init" during SMD simulation

[Alessandra Villa]

HI


However, since I want to pull the protein for a long distance, I should
> gradually change the equilibrium length, and I have no idea how to
> dynamically change the "pull-coord1-init" during SMD simulation. Or do I
> have to restart the simulation with a new .mdp file with different
> "pull-coord1-init" for each step?
>
>
>
To change the pulling coordination during the simulation you can apply a
rate.
pull-coord1-rate [nm/ps]  is the rate of change of the reference position
I suggest to combine with  pull-coord1-init [nm] (that is the reference
distance at t=0).
(see
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html?highlight=freeze%20groups#com-pulling
)
This is also useful to generate starting configurations (at defined
distance values) for the umbrella sampling windows.

Best regards
Alessandra









> Best regards,
> W
> --
> 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.