[gmx-users] [ angle_restraints_z ]

[Berk Hess]

Date: Sat, 17 May 2008 08:48:28 +0330
From: terry.b.nelson at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] [ angle_restraints_z ]

Hi all,


There are atoms (a1 and a2) in my small molecule coordinate file  that have the same z component:

a1: atom#22 (x1,y1,60.231)

a2: atom#45 (x2,y2,60.231)If I use these lines only



Therefore the vector a1-a2 makes theta=90o with the z-axis.  in my
previous MD runs the a1-a2 were flexible (theta was observed in the
range of 30-120 degrees). 

To restrain a1-a2 at this orientation throughout my MD calculations I included these lines to my starting topology:



; Restrain the molecules wrt z-axis...

[ angle_restraints_z ]

; #1 #2  type    theta0(degrees)  k_c(kJ mpl^(-1))  multiplicity

22  45     1       90     1000    1



Would someone comment on:

- Is this is all I need to do to restrain a1-12 wrt z-axis?

- Are the above parameters (theta/K/multiplicity) reasonable/correct?

- with this I should expect a1 and a2 stay in xy-plane (with their z
component equal at each frame) during minimization, equilibration and
production?



Thanks.
-- 
Cheers,
Terry

Did you look at formula 4.68 in the manual?
What you want is a minimum at 90 and maxima at 0 and 180.
So you need to use a multiplicity of 2.
1000 as a force constant seems too large to me, this means that
the 0/180 degrees is penalized by 2000 kJ/mol.

Berk.



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