[gmx-users] Decrease position restraints force constant on the fly

Dawid das addiw7 at googlemail.com
Mon Mar 12 16:20:38 CET 2018


Hi Zheng,

No, I'm not trying to do steered MD, but rather step by step release my
protein backbone atoms from  position restraints.

Thanks, both of you!

Best wishes,
Dawid

2018-03-12 15:47 GMT+01:00 Zheng Ruan <zruan1991 at gmail.com>:

> Hi Dawid,
>
> If I understand correctly, you may able to control the restraint using
> plumed. Check the "Moving on a more complex path" in this tutorial (
> https://plumed.github.io/doc-v2.3/user-doc/html/belfast-5.html).
>
> Ruan
>
> On Mon, Mar 12, 2018 at 10:38 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 3/12/18 10:37 AM, Dawid das wrote:
> >
> >> Dear Gromacs Users,
> >>
> >> Is possible to decrease force constant for position restraints as the MD
> >> simulation progresses? For instance I start with 1000 kJ/(mol *nm2) and
> >> after 20 ps I go
> >> to 800 kJ/(mol*nm2), then after 20 ps to 600 kJ/(mol*nm2), etc.?
> >>
> >
> > No, you have to do individual simulations with different force constants.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Assistant Professor
> > Virginia Tech Department of Biochemistry
> >
> > 303 Engel Hall
> > 340 West Campus Dr.
> > Blacksburg, VA 24061
> >
> > jalemkul at vt.edu | (540) 231-3129
> > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> >
> > ==================================================
> >
> >
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