[gmx-users] Re: suffice of position restraints

[Dr. Vitaly Chaban]

>
> Dear users,
>
> I usually apply the positions restraint of 100 ps on system. Does it
> produce a problem to apply the positions restraint for long time (100 or
> 200 ps)? cant it cause strain on structure?
>
> Thanks in advance


Dear Ahmet Yıldırım -

I believe everything depends on the relation between the restraint
constant(s) and kT.

>From a purely practical experience, we applied position restraints in
microsecond-scale simulations with mild constants, and nothing bad
happened to the structures in the box.

The main application of restraints, from my perspective, is for
genuinely computer experiments, i.e. where we want to simulate
something that cannot be done in experiment for various reasons. If
one wants to derive truly physical values, it is, of course, better to
avoid any restraints.


Dr. Vitaly V. Chaban
MEMPHYS - Center for Biomembrane Physics
Department of Physics, Chemistry and Pharmacy
University of Southern Denmark
Campusvej 55, 5230 Odense M, Denmark