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.



On Wed, Feb 14, 2018 at 8:48 PM, Iman Ahmadabadi <imanahmadabad...@gmail.com
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?


On Wed, Feb 14, 2018 at 5:48 PM, Iman Ahmadabadi <
imanahmadabad...@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.



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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129


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