AMBER: restraints and reordering water

From: Vlad Cojocaru <>
Date: Tue, 11 Nov 2003 10:42:04 +0100

Dear fellow ambers,
    I have a simulation which ran for 7ns (explicit solvent, PME,
Periodic). The structure pretty stable. Now I want to introduce a
restraint over the next 2-3 nanoseconds. I have several questions:
1. Can I do that straight away by just restarting the simulation
starting from the last rst file but using as sander input the file
containing the restraint? Or do I have to consider some other steps
before that?
2. If I have a DISANG file with the restraint it seems that I need a &wt
list. I took a look at the manual and the only thing that I found was
the&wt type='REST' option that is applicable in my case. Could somebody
shortly explain me how this works with "Ramping up the restraints", is
that necessary or can I go with a constant manner of applying the restraint?
3. I got a mssage that "Reordering water will NOT be done" if nmropt>0,
is that ok and what actually does it mean?
Thank you very much in advance for your help!
Best regards,

Vlad Cojocaru 
Max Planck Institute for Biophysical Chemistry 
Department: 060 
Am Fassberg 11, 37077 Goettingen, Germany 
tel: ++49-551-201.1327 
home tel: ++49-551-9963204  
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Received on Tue Nov 11 2003 - 09:53:01 PST
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