AMBER Archive (2009)

Subject: RE: [AMBER] reaction coordinates

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Wed Jan 14 2009 - 23:25:31 CST

Maybe you can try to do potential of mean force calculations (PMF, umbrella sampling in the manual.)> Date: Wed, 14 Jan 2009 08:00:59 -0500> From: case_at_biomaps.rutgers.edu> To: amber_at_ambermd.org> Subject: Re: [AMBER] reaction coordinates> > On Wed, Jan 14, 2009, Rausch, Felix wrote:> > > > I would like to set up a MD simulation with reaction coordinates (distance> > between two atoms), but I'm not sure where I have to put the required> > parameters at in the input file. Unfortunately, the general descriptions in> > the manual don't help me out.> > If you want to add a restraint based on such a distance, these would be> called "NMR" constraints in Amber-ese. Look at the examples in Section> 6.11 of the Users' Manual, and in Tutorial A4..> > Another possibility is ABMD, described in Section 4.6. See tutorial> A10.> > ....dac> > > _______________________________________________> AMBER mailing list> AMBER_at_ambermd.org> http://lists.ambermd.org/mailman/listinfo/amber
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