[gmx-users] Flexible and posres

Justin Lemkul jalemkul at vt.edu
Wed Feb 14 20:55:34 CET 2018

On 2/14/18 2:47 PM, Iman Ahmadabadi wrote:
> Dear Justin,
> Because there is a movement on atoms that posres should act on them, and
> this condition doesn't occur when the flexible option is not used.

Restraints don't prevent movement, only disfavor it. Have you quantified 
this in any way? RMSD? Is there a "Position Rest." energy term written 
to your log file? If so, the restraints are there and acting, but maybe 
you need a different force constant.


> Sincerely,
> Iman
> On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi <imanahmadabadi75 at gmail.com
>> wrote:
>> Dear Mark,
>> I forgot the D in -DPOSRES in the previous email. However I used the
>> "define = -DFLEXIBLE -DPOSRES" but it doesn't work and position restraint
>> was not applied on the atoms. Is there another way to solve the problem?
>> Respectfully,
>> Iman
>> On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi <
>> imanahmadabadi75 at gmail.com> wrote:
>>> Dear Gromacs Users,
>>> If I wanna use some flexible bonds and also use position restraint on
>>> some other atoms, how should I do this? the error arises because 2 define =
>>> -DFLEXIBLE and -POSRES is not allowed in the .mdp files.
>>> Respectfully


Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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