AMBER Archive (2005)

Subject: Re: AMBER: QMMM question

From: xiaoqin huang (xqhuang1018_at_msn.com)
Date: Mon Oct 10 2005 - 13:59:55 CDT

Hi, Guanglei and Ross,
I modified the input file as the attached (pmf1.in), and it runs now.
I want use the reaction coordinate as distance diffence between the
distance(atom6--atom1) and the distance(atom1--atom5), that means the
distance from the CL(ion, -1e) to the C1(carbon in CH3Cl) minus the distance
from C1(carbon in CH3CL) to Cl(chloride in CH3CL). so I defined two
connstraints to track the distance changes, and I removed the other angle
constraints. in addition, I defined the internal constraints to fix three
C-H bonds in CH3Cl.
I hope this way is OK. any suggestions, how do you think about what I
defined.

by the way, this is one window of PMF sampling, if I want to do several
windows, such as 20 windows, how should I define the other runs, is it
simply to run again and again for 20 times? it seems there is no other
parameter to defin the number of runs.

thank you for your good suggestions.

all the best!

xiaoqin

10/10/05


  • text/richtext attachment: pmf1.in
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