RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj

From: Rahaman, Asif <>
Date: Thu, 31 Aug 2006 15:24:43 -0500

Dear All,
Many thanks to Prof. Case, Ross and Simmerlings for helping me out with PBC. It seems that simulation works now. But I still have one problem as follows:
I used IWRAP = 1. When I look at the .rst file with VMD, then I see correct structure of the system. But When I used 'ptraj' to analyze the .crd file, then system looks wired. I think - I am doing something wrong when running 'ptraj'. Here is my (script) file. Could someone please help me find out what I am doing wrong? I have looked at the manual and tried many options without success.
trajin md.crd 1 500 1
trajout traj.crd
box 24.9 24.7 24.7 90.0 90.0 74.8 24.9 24.7 24.7 90.0 90.0 74.8
image center triclinic
I have a crystal block with water molecules with a = 24.9, b=24.7, c=24.7 and \alpha = 90.0,
\beta = 90.0 and \gamma = 74.8. When I run 'ptraj' with above script then the output looks like a cubic box ( not the one as I have specified or I have in the simulation).
How do I look at the trajectory of the system with proper box parameters?
Thank you very much in advance.
With best regards, Asif


From: on behalf of Carlos Simmerling
Sent: Mon 8/28/2006 3:40 PM
Subject: Re: AMBER: Periodic boundary condition (PBC)

a few things to consider-
did you set a periodic system in the mdin file? (NTB)
did you turn on imaging? (IWRAP)
were the initial energies ok? (in the mdout, check initial pressure,
density, etc)

you might want to go through the tutorials on running PBC MD
if you haven't already.
good luck!

Rahaman, Asif wrote:

>Dear All,
>I have read all the information of 'periodic boundary condition' in the AMBER 9 manual and in the mailing list. I have the following difficulties which I could not resolve - I need you guys help.
>I have made a crystal structure with a box ( with sides of different lengths a, b, c and angles \alpha, \beta and \gamma). Then I have created some layers of waters on top of it with similar shape as the crystal ( so now my system has box with sides a, b, c+d and angles \alpha, \beta and \gamma). I used periodic boundary condition (PBC) with same size (a, b, c+d and \alpha, \beta and \gamma). When I run a NVT simulations for a short time, the system goes bizarre - atoms starts flying all over. It seems that there is no PBC
>I have done the following ( as I got this from the AMBER mailing list). 1) I have loaded my PDB file with force modification file in xleap. 2) Then used 'setbox' command to generate the box. 3) then saved the topology and coordinate file. 4) then I have edited the last line of the .crd file to include ( a, b, c+d and \alpha, \beta and \gamma as Dr. Case suggested in the mailing list). But I did not change the same in the topology file.
>Do I need to change the periodic box information in the topology file too? If so could any one please tell me how? Because unlike .crd file .top (topology file) only contains one angle and three sides of the box.
>Is there a special way to create a periodic box with different lengths and box?
>If I am doing anything wrong in simulations, please let me know.
>I did the following before doing NVT simulation:
>I have minimized the system with PBC - It looks fine as structures holds up as expected. Then I have heated the system to 30 K with a NVT run. Then I see atoms are flying all over as if there in no PBC.
>Thank you in advance for you suggestions and comments.
>Best, Asif
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Received on Sun Sep 03 2006 - 06:07:16 PDT
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