From: hl332_at_drexel.edu
Date: Fri May 25 2007 - 11:48:20 CDT
Have you cared to look at old posts? I myself posted this question and also the solution around 10 days back. PLease have a look at that. For your information, you will be using PBCTOOLS plugin of vmd to get any unwrapped coordinates. Google this plugin name and first link takes you to the home page of plugin where you can have a look at several options. I hope it helps.
Harish
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Harish Vashisth (Ph.D Candidate)
CAT-361,Chemical & Biological Engg.
Drexel University, Philadelphia, PA
office: 215-895-5823
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Hello,
In order to get the coordinates of the atoms of one frame in a Molecular Dy=
namics simulation, I am using the script attached.
It seems to work fine, however, when I have periodic boundary conditions, I=
am getting the coordinate values of the periodic atom. Therefore, when I r=
epresent those values, I see the atoms jumping from one side to the other.
I wonder if there is a way to obtain the global coordinate values of the at=
oms.
Thank you
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<HTML dir=3Dltr><HEAD></HEAD>
<BODY>
<DIV><FONT face=3DArial color=3D#000000 size=3D2>Hello,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>In order to get the coordinates of the ato=
ms of one frame in a Molecular Dynamics simulation, I am using the script a=
ttached.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>It seems to work fine, however, when I hav=
e periodic boundary conditions, I am getting the coordinate values of the p=
eriodic atom. Therefore, when I represent those values, I see the atoms jum=
ping from one side to the other.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>I wonder if there is a way to obtain the g=
lobal coordinate values of the atoms.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Thank you</FONT></DIV></BODY></HTML>
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