AMBER Archive (2009)

Subject: Re: [AMBER] Setting a constrain in one direction

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Thu Aug 27 2009 - 22:40:54 CDT

Dear Darren,

I haven't used AMBER for MD, but if you're finding it difficult to do
this in AMBER, you could try using NAMD. It is available at no cost
from a group at UIUC.

It is compatible with the AMBER force field and AMBER-formatted
parameter-topology files. Within NAMD it's pretty simple to impose
harmonic constraints for any selection of atoms in the Z direction
using either the "tclForces" or tclBCforces" commands.

I could send you some examples if you need help, although good
tutorials are available for both NAMD in general and TCL Forces in
particular.

Of course, someone more familiar with AMBER itself may be able to help
you in a more direct way.

Best of luck!

Nicholas Musolino

---------------------------------------------------------------------------
Nicholas Musolino
Ph.D. candidate, Department of Chemical Engineering, MIT
musolino_at_mit.edu | 617-253-6675 | Room E19-528

On Aug 27, 2009, at 11:15 PM, Darren Yang wrote:

> Hi, Amber users.
>
> I need help setting up a special type of MD simulation. Basically, I
> want to
> have one atom in my system able to move in a plane (X/Y for
> example), and
> have a harmonic potential constrain in the Z direction. I am not
> quite sure
> how to do this or if there is a way?
>
> Any suggestion will be greatly appreciated!
> Darren
> ydarren_at_gmail.com
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