Re: Harmonic restraints on distances in sander

From: Vickie Tsui <>
Date: Wed 8 Mar 2000 11:52:57 -0800 (PST)

> I guess my question is whether I can put the restraint information right after
> the dynamics information in an input file, as i did above. Also do the atom

Yes, you can put the restraint information in the input file instead of in
a separate restraint file. You should put the information after the file
redirection commands (see section 3 of sander), and these file redirection
commands must come after the weight changes (section 2 of sander). A
sample input file could look like:

   nmropt=1, pencut=-1, imin=0, nstlim=10000, etc...,
 &wt type='REST', istep1=0, istep2=1000, value1=0.1, value2=1.0, &end
 &wt type='REST', istep1=1001, istep2=10000, value1=1.0, value2=1.0, &end
 &wt type='END' &end
 &rst iat= 39, 51, r1=..., &end

> numbers 3 and 5 correspond to the order of atoms in the topology file? From your
> last message I gather they do.

Yes, they do.


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Received on Wed Mar 08 2000 - 11:52:57 PST
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