To my knowledge, that type of constraint is not available. AMBER generally
lacks the ability to apply robust constraints beyond simple distance
constraints using SHAKE (and even then, only between atoms). I'll speculate
that this is for performance reasons.
Regards,
Brian
On Wed, Jun 18, 2014 at 11:47 AM, Ylenia Cau <cau.ylenia.gmail.com> wrote:
> Dear amber users,
>
> I need help setting up my MD simulation.
> Basically I want to constraint my molecule on the z axis (specific depth in
> a phospholipid membrane) and leave it free to move in the x and y planes.
>
> Any suggestion will be greatly appreciated!!
>
> Ylenia
>
> --
> *Ylenia Cau, PhD Student*
> *Department of Biotechnology, chemistry and pharmaceutical sciences, *
> *University of Siena, Via a Moro 2, 53100 Siena, Italy*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for
Integrative Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
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Received on Wed Jun 18 2014 - 09:30:03 PDT
