Re: [AMBER] Setting up z-constraint

From: Benjamin D Madej <>
Date: Fri, 20 Jun 2014 02:40:27 +0000

.Ylenia: The only option that is currently supported in Amber is to use distance restraints like in umbrella sampling. Note that group restraints are currently not available in the GPU-accelerated pmemd.cuda code, so you are limited to pmemd and pmemd.MPI.

.Brian: It is correct that SHAKE is only available for hydrogen bonds or a set of bonds between atoms. It is currently not possible to constrain molecules or groups of molecules with SHAKE.

.Pierpaolo: Is that all that you changed in the source code? I think this should be added as an official option to Amber so that any combination of X Y Z restraints can be selected.

All the best,
Ben Madej
UCSD Chemistry and Biochemistry
From: Pierpaolo Cacciotto []
Sent: Wednesday, June 18, 2014 10:03 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Setting up z-constraint

Dear Ylenia,

I had almost the same problem and I partially solved it for the pmemd cpu
version in the following way:
(The changes in the link are now working...I just made some mistakes
recompiling the program).


> 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

Pierpaolo Cacciotto - PhD Student
Department of Physics
University of Cagliari
Cittadella Universitaria
09042 Monserrato - Italy
Phone: +39 070 675 4839
AMBER mailing list
AMBER mailing list
Received on Thu Jun 19 2014 - 20:00:02 PDT
Custom Search