[gmx-users] Position Restraints with NVT and NPT

[Mark Abraham]

The restraints just push on the atoms. If other stuff pushes harder, then
the restraints don't work. More relevant is whether you think your starting
position models something with accuracy down to a resolution of 0.01nm, or
some aspect of the starting position is sensitive to such a difference.
(Answer: if it came from an experiment or a simulation, no)

Mark


On Mon, Apr 21, 2014 at 8:41 AM, zanemarkson <zheng.ma at duke.edu> wrote:

> Thank you Justin!
>
> I understand usually for regular equilibration, restraints should be
> enough.
> But I am still wondering to what extent position restraint can restrain my
> atoms. In fact, I ran a relatively longer NVT using position restraints and
> I saw that both the absolute coordinates of my "restrained" atoms and the
> distances between my "restrained" atoms changed by ~0.01nm and I think that
> is not negligible any more. I don't know whether this is normal or a
> problem
> that I should somehow fix. Any thoughts? Thank you!
>
> --
> View this message in context:
> http://gromacs.5086.x6.nabble.com/Position-Restraints-with-NVT-and-NPT-tp5015953p5015961.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> 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.
>