**From:** Eric H. Lee (*ericlee_at_ks.uiuc.edu*)

**Date:** Tue May 12 2009 - 01:15:56 CDT

**Next message:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Previous message:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**In reply to:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Next in thread:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Reply:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Yes, from the VMD File menu once you've finished unwrapping it.

On May 12, 2009, at 1:07 AM, Fred (Rui FENG) wrote:

*> Thank you Eric and Joshua! It's what I need. I have a quite large
*

*> DCD file (more than 10 GB), so I will do it frame by frame. Can I
*

*> save the unwrapped atoms to a new DCD file?
*

*>
*

*> Fred
*

*>
*

*> On Tue, May 12, 2009 at 12:49 AM, Eric H. Lee <ericlee_at_ks.uiuc.edu>
*

*> wrote:
*

*> You can choose not to wrap the system coordinates during the
*

*> simulation, but keeping the periodic boundary conditions in place.
*

*> The options in the namd script are "wrapall" and "wrapwater" I
*

*> believe.
*

*>
*

*> You might also try unwrapping your existing trajectory using PBCtools:
*

*>
*

*> http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
*

*>
*

*> -Eric
*

*>
*

*> On May 11, 2009, at 11:26 PM, Fred (Rui FENG) wrote:
*

*>
*

*>> Hi All,
*

*>>
*

*>> I have a question that can be simplified like this:
*

*>>
*

*>> Suppose there's a cube with lots of particles/atoms. The boundary
*

*>> is periodic and only Lennard Jones force field is in the system.
*

*>> All atoms are moving with random velocities. The velocity of the
*

*>> center of mass could not be zero. I have a common DCD file with
*

*>> coordinates of all atoms. My question is: how to get the
*

*>> displacement of all atoms?
*

*>>
*

*>> I cannot just simply subtract the coordinate of one atom from the
*

*>> coordinate of the same atom in the previous frame. Supposing the
*

*>> cube has 200 edge length and the center is (0,0,0). If a atom at
*

*>> the position (99, 0, 0) moves to the position (-99, 0, 0), the
*

*>> displacement could be either 2 or -198 because of the periodic
*

*>> boundary. The absolute coordinate could be (102, 0, 0), but in the
*

*>> DCD file it's (-99, 0, 0). It makes the displacement calculation
*

*>> impossible.
*

*>>
*

*>> So I was wondering if there are any ways with which NAMD can output
*

*>> a "modified" DCD file with absolute coordinates. Thank you!
*

*>>
*

*>> Have a nice day!
*

*>>
*

*>> Fred
*

*>
*

*> Eric H. Lee
*

*> Medical Scholars Program
*

*> Theoretical and Computational Biophysics Group, UIUC
*

*> ericlee_at_ks.uiuc.edu
*

*>
*

*>
*

Eric H. Lee

Medical Scholars Program

Theoretical and Computational Biophysics Group, UIUC

ericlee_at_ks.uiuc.edu

**Next message:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Previous message:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**In reply to:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Next in thread:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Reply:**Fred (Rui FENG): "Re: Calculating displacement in a system with periodic boundary"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Wed Feb 29 2012 - 15:52:46 CST
*