[gmx-users] [ angle_restraints_z ]
Berk Hess
gmx3 at hotmail.com
Mon May 19 15:04:09 CEST 2008
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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