RE: AMBER: constrains

From: Ross Walker <>
Date: Mon, 14 Feb 2005 09:10:42 -0800

Dear Gustavo,
   I found the problem that I have with the dynamics. I hed started eith the
systems with constraints in CA atoms at 300 K. When I tried to take out the
constrains, I did it in an abrupt manner and the rms exploted. What I need
is to take off the constrains slowly. How can I do it?
Presicely, I need to do what I did with the temperature (&wt type="temp0",
value1=... &end ; &wt type="temp0", valu1=... &end) but with the constrains.
But I donīt know how to tell the program to take out the constrains slowly
I don't believe you can do this in an automated way. Somebody correct me if
I am wrong. The best option would be to write a number of input files, say
10 or so. All reading from the restrt file of the previous one but with
progressively weaker and weaker constraints. E.g.
20,15,10,5,3,1,0.1,0.001,0.001, 0.0001.
Each should probably run for about 5 or 10ps or so.
You can automate them via a shell script if you want.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Feb 14 2005 - 17:53:01 PST
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