[gmx-users] Position restrained energy minimization

Peter Kroon p.c.kroon at rug.nl
Thu Feb 7 12:49:52 CET 2019

That will still allow peptide atoms to move (if only a little).

AFAIK Gromacs is not really fit for rigid body studies, but you can set
all bonds and angles to constraints (mdp option:
constraints=all-angles). This may or may not work. Torsion angles will
still be free to rotate though. From the manual [1], emphasis mine:



        LINear Constraint Solver. With domain decomposition the parallel
        version P-LINCS is used. The accuracy in set with |lincs-order|
        which sets the number of matrices in the expansion for the
        matrix inversion. After the matrix inversion correction the
        algorithm does an iterative correction to compensate for
        lengthening due to rotation. The number of such iterations can
        be controlled with |lincs-iter|
        The root mean square relative constraint deviation is printed to
        the log file every |nstlog|
        <http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#mdp-nstlog> steps.
        If a bond rotates more than |lincs-warnangle|
        <http://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#mdp-lincs-warnangle> in
        one step, a warning will be printed both to the log file and
        to |stderr|. *LINCS should not be used with coupled angle


        SHAKE is slightly slower and less stable than LINCS, but does
        work with angle constraints. The relative tolerance is set
        with |shake-tol|
        0.0001 is a good value for “normal” MD. SHAKE does not support
        constraints between atoms on different nodes, thus it can not be
        used with domain decompositon when inter charge-group
        constraints are present. *SHAKE can not be used with energy

Maybe someone else has a genius idea on how to treat your peptide as a
rigid body during minimization. Also, *why* is it important for your
analysis that the internal coordinates of your peptide do not change?



On 07-02-19 12:35, Quyen Vu wrote:
> When you run EM with -v directive, you will see how much is the largest
> force value applies to your atom. Try to estimate whether that force
> constant was enough to keep your atom fix because if your structure has any
> overlap, force can be very large
> On Thu, Feb 7, 2019 at 6:40 AM Ashraya Ravikumar <ashrayar at gmail.com> wrote:
>> Hi,
>> I am trying to do position restrained energy minimization of a solvated
>> peptide, where the peptide is restrained but the solvent is free to move.
>> But I do see the positions of the atoms of the peptide change. I increased
>> the force value in position restraint file to 10000 from 1000, but it
>> doesn't help. It is important for my analysis that the internal bond
>> parameters (bond lengths, angles, and torsion angle) of the peptide do not
>> change from its initial values. Is there any solution for this?
>> Thanks in advance.
>> Regards,
>> Ashraya
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